Methods and kits to identify Klebsiella strains

ABSTRACT

The present invention provides a method of detecting one or more  Klebsiella  species within a sample from a subject, the method comprising: subjecting DNA and/or RNA from the sample to a PCR amplification reaction using primer pairs targeting species-specific canonical single nucleotide polymorphisms (canSNPs); and analyzing amplification products resulting from the PCR amplification reaction to detect the one or more  Klebsiella  species. The present invention also provides a kit for detection of one or more  Klebsiella  species,  Klebsiella  clonal groups, AMR genes, and/or virulence genes, the kit comprising primer pairs targeting species-specific canSNPs,  K. pneumoniae  genes M1 and M2, clonal group-specific canSNPs, AMR genes, and/or virulence genes.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is the U.S. National Stage of International Application No. PCT/US2017/022211, filed on Mar. 14, 2017, which claims priority to and the benefit of U.S. Provisional Application Ser. No. 62/307,632, filed on Mar. 14, 2016, the contents of each of which are hereby incorporated by reference in their entireties.

GOVERNMENTAL SUPPORT OF APPLICATION

This invention was made with governmental support under grant number R01AI090782 awarded by the National Institutes of Health (NIH). The United States government has certain rights in the invention.

REFERENCE TO SEQUENCE LISTING SUBMITTED ELECTRONICALLY

The official copy of the sequence listing is submitted electronically via EFS-Web as an ASCII-formatted sequence listing with a file named “91482_210_Sequence_Listing.txt” created on Mar. 13, 2017, and having a size of 50 kilobytes, and is filed concurrently with the specification. The sequence listing contained in this ASCII-formatted document is part of the specification and is herein incorporated by reference in its entirety.

TECHNICAL FIELD

The present invention relates to the field of detection of Klebsiella species that cause health care-acquired infection (HAI) in patients and healthcare workers.

BACKGROUND

Klebsiella pneumoniae has been a leading HAI agent for decades (1, 2). The emergence of multidrug-resistant K. pneumoniae, especially extended-spectrum β-lactamase (ESBL) producers and carbapenemase producers, has elevated the morbidity and mortality rates and health care costs associated with K. pneumoniae to highly significant levels (3-6). Health care- and outbreak-associated strain types of K. pneumoniae that appear highly transmissible and have a propensity for antimicrobial resistance (AMR) or virulence gene acquisition are a growing proportion of the K. pneumoniae species (7-18). Sequence type 258 (ST258), the crux of the worldwide carbapenemase-producing Enterobacteriaceae (CPE) threat, has disseminated rapidly around the world's health care systems despite its recent emergence (17). Its progenitor strains in clonal group 258 (CG258) also cause outbreaks and carry many important ESBL- and carbapenemase-encoding genes (9, 19-21). Several other strain types, such as those in CG14, CG20, and CG37, also frequently appear as multidrug resistant and in outbreak situations (7, 10, 12, 15).

Host colonization is likely an important reservoir driving the transmission of these strains. In the health care environment, intestinal colonization of K. pneumoniae is a risk factor for infection (22-24), and carriers of CPE are at high risk for invasive disease (25). Rates of CPE and ESBL-producing K. pneumoniae colonization are rising in patient and health care worker populations, increasing the size of the reservoir and increasing chances of transmission (26, 27). Asymptomatic transmission of multidrug-resistant strains is rapid (16, 28), and transmission events that lead to outbreaks often go undetected (29, 30). Early detection of K. pneumoniae colonization of patients, especially multidrug-resistant K. pneumoniae or epidemic strain type colonization, is now considered critical to infection control (24, 30-33).

Infection control programs that include the detection and isolation of carriers have repeatedly been successful in markedly decreasing multidrug-resistant or epidemic strain infections (31, 34-37), but this practice is uncommon for several reasons. Many of these programs use culture-based methods for detecting CPE or ESBL producers, which have several limitations, including turnaround time, narrow application, fair sensitivity and specificity, and extensive labor for high-throughput screening (31, 38). PCR-based assays are rapid but often use DNA from culture, and a limited number of tests can be run simultaneously, potentially missing important AMR genes not previously known to circulate in a given locale (31, 39).

Next-generation sequencing has gained a foothold in health care with whole-genome sequencing (WGS) for outbreak detection, transmission mapping, and source tracing (40, 41), microbiome sequencing (e.g., targeted 16S rRNA gene sequencing) to understand microbial population structure (42, 43) and with metagenomic sequencing to attempt to determine all of the genetic factors present (44). Although metagenomic sequencing does not require an a priori understanding of the genetic targets in a clinical sample, it does have significant drawbacks, limiting its translation to the clinical microbiology laboratory. Chief among these are that (i) the required amount of sequencing space increases the cost and time, (ii) limited coverage across targets lessens the confidence in diagnostic calls, and (iii) the necessary computing power and highly complex analysis limit the ability for local analysis. Targeted amplicon sequencing, on the other hand, allows for rapid, cost-effective, highly multiplexed, and accurate detection of numerous clinically important targets directly in clinical samples (45). Such assays have recently been approved by the FDA for clinical diagnostics (46). There is a continuing need for compositions and methods for the diagnosis of HAI caused by Klebsiella species that address these challenges to efficient detection and treatment.

SUMMARY

HAIs kill tens of thousands of people each year and add significantly to health care costs. Multidrug-resistant and epidemic strains are a large proportion of HAI agents, and multidrug-resistant strains of Klebsiella pneumoniae, a leading HAI agent, have caused an urgent public health crisis. In the health care environment, patient colonization by K. pneumoniae precedes infection, and transmission via colonization leads to outbreaks. Periodic patient screening for K. pneumoniae colonization has the potential to curb the number of HAIs.

The present invention provides a new amplicon sequencing tool, KlebSeq, for screening and surveillance that detects and characterizes Klebsiella bacteria in complex samples such as wound and nasal swabs or fecal samples without culturing. KlebSeq includes a sizeable panel of assays for species identification, strain identification, and important AMR and virulence gene targets designed to generate information for health care epidemiology and infection prevention. KlebSeq also includes an analysis pipeline for instant interpretation of the data. Results from the screening of a patient population with this system would rule in or rule out the possibilities of particular transmission events and identify patients carrying high-risk strains like ST258 or other multidrug-resistant Klebsiella strains. The highly multiplexed nature of KlebSeq greatly expands the capacity of a single sequencing run, minimizing costs, and allows for high-throughput patient sample testing.

Herein, we describe the design and validation of KlebSeq, a highly informative screening tool that detects Klebsiella species and identifies clinically important strains and characteristics by using highly multiplexed amplicon sequencing without a live-culturing step. We demonstrate the utility of this tool on several complex specimen types, including urine, wound swabs and tissue, and several types of respiratory and fecal specimens, showing K. pneumoniae species and clonal group identification and antimicrobial resistance and virulence profiling, including capsule typing. Use of this amplicon sequencing tool to screen patients for Klebsiella carriage could inform health care staff of the risk of infection and outbreak potential. KlebSeq also serves as a model for next-generation molecular tools for public health and health care, as expansion of this tool can be used for several other HAI agents or applications.

In some embodiments, the present invention provides a method of detecting one or more Klebsiella species within a sample from a subject, the method comprising: subjecting DNA and/or RNA from the sample to a PCR amplification reaction using primer pairs targeting species-specific canonical single nucleotide polymorphisms (canSNPs); and analyzing amplification products resulting from the PCR amplification reaction to detect the one or more Klebsiella species.

In other embodiments, the method further comprises subjecting DNA and/or RNA from the sample to a PCR amplification reaction using primer pairs targeting K. pneumoniae genes M1 and M2; and analyzing amplification products resulting from the PCR amplification reaction to detect the K. pneumoniae genes M1 and M2.

In yet other other embodiments, the primer pairs comprise a universal tail sequence. In one embodiment, the primer pairs contain sequences selected from the group consisting of SEQ ID NOs: 1-10.

In some aspects, the one or more Klebsiella species are selected from the group consisting of K. pneumoniae, K. quasipneumoniae, K. oxytoca, and K. variicola.

In other aspects, the method further comprises detecting one or more Klebsiella clonal groups in the sample by subjecting DNA and/or RNA from the sample to a PCR amplification reaction using primer pairs targeting clonal group-specific canSNPs and analyzing amplification products resulting from the PCR amplification reaction to detect the one or more Klebsiella clonal groups.

In yet other aspects, the primer pairs targeting clonal group-specific canSNPs contain sequences selected from the group consisting of SEQ ID NOs: 11-84.

In other embodiments, the method further comprises detecting one or more antimicrobial resistance resistance (AMR) genes in the Klebsiella species in the sample by subjecting DNA and/or RNA from the sample to a PCR amplification reaction using primer pairs targeting AMR genes and analyzing amplification products resulting from the PCR amplification reaction to detect the one or more AMR genes.

In yet other embodiments, the primer pairs targeting AMR genes contain sequences selected from the group consisting of SEQ ID NOs: 85-248.

In some implementations, the method further comprises detecting one or more virulence genes in the Klebsiella species in the sample by subjecting DNA and/or RNA from the sample to a PCR amplification reaction using primer pairs targeting virulence genes and analyzing amplification products resulting from the PCR amplification reaction to detect the one or more virulence genes. In one implementation, the primer pairs targeting virulence genes contain sequences selected from the group consisting of SEQ ID NOs: 249-281.

In certain aspects, the PCR amplification reaction is a multiplex amplification reaction. In other aspects, the amplification products are analyzed by next-generation sequencing (NGS) to determine the sequence of each amplification product.

In yet other aspects, the sample is a wound swab, a nasal swab, rectal swab, skin swab, saliva, feces, urine, whole blood, serum, plasma, or buffy coat.

In some embodiments, the subject is an animal. In one embodiment, the animal is a human.

In other aspects, the present invention is directed to a kit for detection of one or more Klebsiella species, Klebsiella clonal groups, AMR genes, and/or virulence genes, the kit comprising primer pairs targeting species-specific canSNPs, K. pneumoniae genes M1 and M2, clonal group-specific canSNPs, AMR genes, and/or virulence genes.

In some aspects, the primer pairs comprise a universal tail sequence. In one aspect, the primer pairs contain sequences selected from the group consisting of SEQ ID NOs: 1-281. In yet another aspect, the kit further comprises a nucleotide polymerase, buffer, diluent, and/or excipient.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 depicts a workflow of the amplicon sequencing target library and assay development pipeline.

FIG. 2 depicts a partial sample output of KlebSeq ASAP report; some AMR gene assays and the virulence gene assays are hidden from view to limit the size of the image. The top box shows a summary of what was detected according to selected ASAP filters. Details of each assay appear below that. If additional SNPs are detected in comparison to the assay reference, hovering over “details . . . ” expands a list of the SNPs. Clicking on an assay name pops up a graph of coverage depth across the reference sequence.

FIG. 3 depicts a workflow of the validation of KlebSeq. Dotted lines are methods used to confirm results from the workflow in solid lines (KlebSeq of specimen DNA). Strain identification validation was performed for 73 isolates plus 6 isolates that were cultured from KlebSeq-tested specimens (Tables 2 and 3). MLST PCR and sequencing were performed with 11 specimen DNA samples (Table 3). AMR gene detection validation is described in the text. NGS refers to next-generation sequencing.

FIG. 4 depicts a maximum-parsimony tree with 100 bootstraps of the SNPs among 548 K. pneumoniae genomes. Major clonal groups are colored, and locations of canSNPs for strain identification assays are marked with stars. All of the branches labeled with canSNPs had >99% bootstrap support, except for the three branches indicated.

FIG. 5 depicts a neighbor-joining tree with 100 bootstraps of the SNPs in the diverse set of K. pneumoniae, K. variicola, and K. quasipneumoniae genomes used in this study. Unknown isolates that were identified as K. variicola and K. quasipneumoniae are boxed.

DETAILED DESCRIPTION

As used herein, the verb “comprise” as is used in this description and in the claims and its conjugations are used in its non-limiting sense to mean that items following the word are included, but items not specifically mentioned are not excluded. In addition, reference to an element by the indefinite article “a” or “an” does not exclude the possibility that more than one of the elements are present, unless the context clearly requires that there is one and only one of the elements. The indefinite article “a” or “an” thus usually means “at least one”.

As used herein, “amplification reaction” refers to a method of detecting target nucleic acid by in vitro amplification of DNA or RNA.

As used herein, “polymerase chain reaction (PCR)” refers to the amplification of a specific DNA sequence, termed target or template sequence, that is present in a mixture, by adding two or more short oligonucleotides, also called primers, that are specific for the terminal or outer limits of the template sequence. The template-primers mixture is subjected to repeated cycles of heating to separate (melt) the double-stranded DNA and cooling in the presence of nucleotides and DNA polymerase such that the template sequence is copied at each cycle.

The term “primer” refers to DNA oligonucleotides complementary to a region of DNA and serves as the initiation of amplification reaction from the 5′ to 3′ direction.

The term “primer pair” refers to the forward and reverse primers in an amplification reaction leading to amplification of a double-stranded DNA region of the target.

The term “target” refers to a nucleic acid region bound by a primer pair that is amplified through an amplification reaction. The PCR “product” or “amplicon” is the amplified nucleic acid resulting from PCR of a set of primer pairs.

The term “multiplex amplification reaction” herein refers to the detection of more than one template in a mixture by the addition of more than one set of oligonucleotide primers.

In certain aspects, the methods and kits of the present invention are used as a surveillance tool for a health care facility. If the KlebSeq assays, methods, and/or kits produce positive results (i.e., detect the presence of the Klebsiella species, clonal group, AMR gene, and/or virulence gene) this result could be used be to limit the subsequent infection and transmission of the pathogenic organism to another patient or health care worker. The specific measures taken would depend on the facility.

In other aspects, the KlebSeq assays, methods, and/or kits disclosed herein are used as a diagnostic tool. Upon detection of a positive result in a subject, the subject is treated with an antibiotic regimen. In one aspect, the antibiotic regimen depends on which assays are positive and/or on the facility.

In one embodiment, in cases of detection of pneumonia caused by Klebsiella the subject is treated with aminoglycosides and/or cephalosporins. In another embodiment, with results indicating ESBL production by the Klebsiella the subject is treated with carbapenem. In some aspects, the specific treatment also depends on which organ system is affected.

In some embodiments, a threshold is used to generate a positive result. In one aspect, an amplicon sequence must match the reference sequence at the threshold or above in order to know that the organism being identified is indeed what the assay tests for. For example, if the threshold is 97% for a Klebsiella pneumoniae assay, then amplicon sequences that are less than 97% identical to the reference sequence will be ignored, as they represent organisms that are not Klebsiella pneumoniae and are a negative result on the assay. Sequences at 97% or greater similarity to the reference are a positive result for the Klebsiella pneumoniae assay. This may be particularly useful for certain assays where there is cross-reactivity of the primers with non-targets, but amplicon sequencing can distinguish targets from non-targets.

In some aspects, the threshold is about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99% or about 100%.

As described in greater detail herein, some embodiments of the invention may include amplicon-based sequencing of the one or more markers to make the aforementioned determinations. Some embodiments of the invention include systems and methods of preparing samples for one or more downstream processes that can be used for assessing one or more markers for any of the previously mentioned purposes. Some embodiments of the invention may comprise a universal indexing sequencing strategy for use in downstream sequencing platform processes. By way of example only, some embodiments of the invention comprise a universal indexing sequencing strategy that can be used to amplify multiple genomic regions (e.g., markers, as described below) from a DNA sample simultaneously in a single reaction for the sequencing of one or more amplicons. One or more embodiments of the invention can be used with any desired sequencing platform, such as the ILLUMINA® Next Generation Sequencing (e.g., MiSEQ) platform, Life Technologies' Ion Torrent System, or any other sequencing system now known or developed in the future.

Some embodiments may be configured to enable relatively simple, rapid (e.g., microorganism-culture independent), inexpensive, and efficient preparation of samples for use on, in, and/or with downstream sequencing platforms. For example, some embodiments may use a sequence coupled to one or more oligonucleotides/primers (as used herein, oligonucleotides and primers are used interchangeably). More specifically, one or more amplicons per sample can be generated using a hybrid oligonucleotide that is designed for amplification of a marker and incorporation of at least one universal tail sequence into the resulting amplicon. As a result, additional steps that may be conventionally required to prepare samples for sequencing can be limited or removed entirely. Further information regarding the universal tail, amplicon-based sequencing strategy can be found in PCT/US2014/064890, which is hereby incorporated by reference in its entirety for all purposes.

In some embodiments, the methodology may include performing downstream sequencing on one or more amplicons. For example, in order to minimize and/or eliminate the need for cultures of microorganisms or large inputs of nucleic acids, methodologies of the instant invention may include an initial PCR step to create amplicons that correspond to the one or more pre-selected markers. As such, some embodiments require only limited amounts of starting material are necessary and the starting material need not be of high quality (e.g., genomic DNA, crude DNA extracts, single stranded DNA, RNA, cDNA, etc.). In contrast, many conventional sample preparation systems may require relatively large amounts of starting material of relatively high quality, which can limit the use of some conventional systems.

Some embodiments of the invention can be used for and/or in complement with high-throughput amplicon sequencing of markers, which can be very useful for a variety of molecular genetic genotyping/predicted-phenotyping applications, including clinical sample analysis. For example, use of the systems and methods of the invention can be employed with sequencing platforms to provide rapid, high-yield sequence data, which can enable the sequencing of multiple markers/amplicons from many samples in a relatively short period of time. Specifically, in some embodiments, amplicons can be selected and PCR reactions can be designed to provide information that can be used to make clinically relevant determinations after sequencing of the amplicons.

In some preferred aspects, the methodology may include creating a series of oligonucleotides designed to provide multiplexed amplification of one or more markers to produce the desired amplicons. In particular, the one or more markers and amplicons thereof can be selected/amplified to provide users with clinically relevant information related to identification of one or more potentially infectious microorganisms and phenotypic and genotypic information about the microorganisms. After production of the amplicons (e.g., via PCR amplification), which may include the universal tail sequences, the method may include processing the resulting amplicons for downstream sequencing and thereafter sequencing the processed amplicons. After processing and analysis of the resulting sequencing data, one of skill in the art can make any necessary determinations regarding the identification of one or more microorganisms that may have been contained within the sample and predicted-phenotypic and/or genotypic information revealed.

Generally, some embodiments of the present invention can be used to detect, identify, assess, sequence, or otherwise evaluate a marker. A marker may be any molecular structure produced by a cell, expressed inside the cell, accessible on the cell surface or secreted by the cell. A marker may be any protein, carbohydrate, fatty acid, nucleic acid, catalytic site, or any combination of these such as an enzyme, glycoprotein, cell membrane, virus, a particular cell, or other uni- or multimolecular structure. A marker may be represented by a sequence of a nucleic acid or any other molecules derived from the nucleic acid. Examples of such nucleic acids include miRNA, tRNA, siRNA, mRNA, cDNA, genomic DNA sequences, single-stranded DNA, or complementary sequences thereof. Alternatively, a marker may be represented by a protein sequence. The concept of a marker is not limited to the exact nucleic acid sequence or protein sequence or products thereof; rather it encompasses all molecules that may be detected by a method of assessing the marker. Without being limited by the theory, the detection, identification, assessment, sequencing, or any other evaluation of the marker may encompass an assessment of a change in copy number (e.g., copy number of a gene or other forms of nucleic acid) or in the detection of one or more translocations. Moreover, in some embodiments, the marker may be relevant to a particular phenotype or genotype. By way of example only, in some embodiments, the marker may be related to phenotypes including antibiotic resistance, virulence, or any other phenotype.

Therefore, examples of molecules encompassed by a marker represented by a particular sequence further include alleles of the gene used as a marker. An allele includes any form of a particular nucleic acid that may be recognized as a form of the particular nucleic acid on account of its location, sequence, or any other characteristic that may identify it as being a form of the particular gene. Alleles include but need not be limited to forms of a gene that include point mutations, silent mutations, deletions, frameshift mutations, single nucleotide polymorphisms (SNPs), inversions, translocations, heterochromatic insertions, and differentially methylated sequences relative to a reference gene, whether alone or in combination. An allele of a gene may or may not produce a functional protein; may produce a protein with altered function, localization, stability, dimerization, or protein-protein interaction; may have overexpression, underexpression or no expression; may have altered temporal or spatial expression specificity; or may have altered copy number (e.g., greater or less numbers of copies of the allele). An allele may also be called a mutation or a mutant. An allele may be compared to another allele that may be termed a wild type form of an allele. In some cases, the wild type allele is more common than the mutant.

In some aspects, the markers may include one or more sets of amplifiable nucleic acids that can provide diagnostic information about the microorganisms. For example, the markers may include amplifiable nucleic acid sequences that can be used to assess the presence and/or absence of one or more microorganism that may have the potential to cause a diseased state in the subject. In some embodiments, the markers may include amplifiable nucleic acid sequences that can be used to identify one or more of the following exemplary microorganisms: Klebsiella spp. (including but not limited to K. granulomatis, K. oxytoca, K. pneumoniae, K. terrigena, and K. variicola).

In some embodiments, the methods may include the use of one or more than one marker per microorganism. Moreover, in some embodiments, one or more of the microorganisms may not be considered pathogenic to certain subjects, but the methodology employed herein can still rely on detection of pathogenic and non-pathogenic microorganisms for differential diagnoses/diagnostics. In some embodiments, the oligonucleotides (with or without the universal tail sequences detailed herein) listed in Table 4 can be used with embodiments of the invention to amplify one or more markers from the microorganisms to provide diagnostic/identification information to the user.

Moreover, in some embodiments, one or more the markers associated with the plurality of microorganisms can be amplified in a multiplex manner. For example, in some aspects, nucleic acids can be obtained from the sample and the oligonucleotides used to amplify one or more of the markers used to identify/diagnose can be added to a single mixture to produce a plurality of amplicons in a single reaction mixture. In other aspects, the oligonucleotides can be added to multiple mixtures to provide for the creation of multiple amplicons in multiple mixtures.

Moreover, in some embodiments, one or more the markers can be amplified in a multiplex manner. For example, in some aspects, nucleic acids can be obtained from the sample and the oligonucleotides used to amplify one or more of the markers used to identify the strain of the microorganism can be added to a single mixture to produce a plurality of amplicons in a single reaction mixture. In other aspects, the oligonucleotides can be added to multiple mixtures to provide for the creation of multiple amplicons in multiple mixtures. In some aspects, amplification of the markers used to identify microorganisms/diagnose an infection can also occur in a multiplex manner such that some or all of the amplicons are generated in a single reaction for a particular sample. In other aspects, amplification of the markers used to identify microorganisms/diagnose an infection can occur in multiple reaction vessels. Overall, as described in greater detail below, regardless of the multiplex nature of some embodiments of the invention, after amplification of the markers, the method may include processing and sequencing the resulting amplicons to provide information related to the identification, characterization, and strain identity of one or more microorganisms that may be present within the sample.

Some embodiments of the invention may comprise the use of one or more methods of amplifying a nucleic acid-based starting material (i.e., a template, including genomic DNA, crude DNA extract, single-stranded DNA, double-stranded DNA, cDNA, RNA, or any other single-stranded or double-stranded nucleic acids). Nucleic acids may be selectively and specifically amplified from a template nucleic acid contained in a sample. In some nucleic acid amplification methods, the copies are generated exponentially. Examples of nucleic acid amplification methods known in the art include: polymerase chain reaction (PCR), ligase chain reaction (LCR), self-sustained sequence replication (3SR), nucleic acid sequence based amplification (NASBA), strand displacement amplification (SDA), amplification with Qβreplicase, whole genome amplification with enzymes such as φ29, whole genome PCR, in vitro transcription with T7 RNA polymerase or any other RNA polymerase, or any other method by which copies of a desired sequence are generated.

In addition to genomic DNA, any polynucleotide sequence can be amplified with an appropriate set of primer molecules. In particular, the amplified segments created by the PCR process itself are, themselves, efficient templates for subsequent PCR amplifications.

PCR generally involves the mixing of a nucleic acid sample, two or more primers or oligonucleotides (primers and oligonucleotides are used interchangeably herein) that are designed to recognize the template DNA, a DNA polymerase, which may be a thermostable DNA polymerase such as Taq or Pfu, and deoxyribose nucleoside triphosphates (dNTP's). In some embodiments, the DNA polymerase used can comprise a high fidelity Taq polymerase such that the error rate of incorrect incorporation of dNTPs is less than one per 1,000 base pairs. Reverse transcription PCR, quantitative reverse transcription PCR, and quantitative real time reverse transcription PCR are other specific examples of PCR. In general, the reaction mixture is subjected to temperature cycles comprising a denaturation stage (typically 80-100° C.), an annealing stage with a temperature that is selected based on the melting temperature (Tm) of the primers and the degeneracy of the primers, and an extension stage (for example 40-75° C.). In real-time PCR analysis, additional reagents, methods, optical detection systems, and devices known in the art are used that allow a measurement of the magnitude of fluorescence in proportion to concentration of amplified template. In such analyses, incorporation of fluorescent dye into the amplified strands may be detected or measured.

Either primers or primers along with probes allow a quantification of the amount of specific template DNA present in the initial sample. In addition, RNA may be detected by PCR analysis by first creating a DNA template from RNA through a reverse transcriptase enzyme (i.e., the creation of cDNA). The marker expression may be detected by quantitative PCR analysis facilitating genotyping analysis of the samples.

“Amplification” is a special case of nucleic acid replication involving template specificity. Amplification may be a template-specific replication or a non-template-specific replication (i.e., replication may be specific template-dependent or not). Template specificity is here distinguished from fidelity of replication (synthesis of the proper polynucleotide sequence) and nucleotide (ribo- or deoxyribo-) specificity. Template specificity is frequently described in terms of “target” specificity. Target sequences are “targets” in the sense that they are sought to be sorted out from other nucleic acid. Amplification techniques have been designed primarily for this sorting out. The amplification process may result in the production of one or more amplicons.

The term “template” refers to nucleic acid originating from a sample that is analyzed for the presence of one or more markers. In contrast, “background template” or “control” is used in reference to nucleic acid other than sample template that may or may not be present in a sample. Background template is most often inadvertent. It may be the result of carryover, or it may be due to the presence of nucleic acid contaminants sought to be purified out of the sample. For example, nucleic acids from organisms other than those to be detected may be present as background in a test sample.

In addition to primers and probes, template specificity is also achieved in some amplification techniques by the choice of enzyme. Amplification enzymes are enzymes that, under the conditions in which they are used, will process only specific sequences of nucleic acid in a heterogeneous mixture of nucleic acid. Other nucleic acid sequences will not be replicated by this amplification enzyme. Similarly, in the case of T7 RNA polymerase, this amplification enzyme has a stringent specificity for its own promoters (Chamberlin et al. (1970) Nature (228):227). In the case of T4 DNA ligase, the enzyme will not ligate the two oligonucleotides or polynucleotides, where there is a mismatch between the oligonucleotide or polynucleotide substrate and the template at the ligation junction (Wu and Wallace (1989) Genomics (4):560). Finally, Taq and Pfu polymerases, by virtue of their ability to function at high temperature, are found to display high specificity for the sequences bounded and thus defined by the primers; the high temperature results in thermodynamic conditions that favor primer hybridization with the target sequences and not hybridization with non-target sequences (H. A. Erlich (ed.) (1989) PCR Technology, Stockton Press).

The term “amplifiable nucleic acid” refers to nucleic acids that may be amplified by any amplification method. It is contemplated that “amplifiable nucleic acid” will usually comprise “sample template.” The terms “PCR product,” “PCR fragment,” “amplification product,” and “amplicon” refer to the resultant mixture of compounds after two or more cycles of the PCR steps of denaturation, annealing and extension. These terms encompass the case where there has been amplification of one or more segments of one or more target sequences.

In some forms of PCR assays, quantification of a target in an unknown sample is often required. Such quantification may be determined in reference to the quantity of a control sample. The control sample starting material/template may be co-amplified in the same tube in a multiplex assay or may be amplified in a separate tube. Generally, the control sample contains template at a known concentration. The control sample template may be a plasmid construct comprising only one copy of the amplification region to be used as quantification reference. To calculate the quantity of a target in an unknown sample, various mathematical models are established. Calculations are based on the comparison of the distinct cycle determined by various methods, e.g., crossing points (C_(P)) and cycle threshold values (C_(t)) at a constant level of fluorescence; or C_(P) acquisition according to established mathematic algorithm.

Some embodiments of the invention may comprise a multiplex assay. As used herein, the term “multiplex” refers to the production of more than one amplicon, PCR product, PCR fragment, amplification product, etc. in a single reaction vessel. In other words, multiplex is to be construed as the amplification of more than one marker-specific sequences within a PCR reaction or assay within the same PCR assay mixture (e.g., more than one amplicon is produced within a single vessel that contains all of the reagents necessary to perform a PCR reaction). In some embodiments, a step prior to performing the PCR (or RT-PCR, quantitative RT-PCR, etc.) reaction can occur such that sets of primers and/or primers and probes are designed, produced, and optimized within a given set of reaction conditions to ensure proper amplicon production during the performance of the PCR.

The algorithm for C_(t) values in real time-PCR calculates the cycle at which each PCR amplification reaches a significant threshold. The calculated C_(t) value is proportional to the number of marker copies present in the sample, and the C_(t) value is a precise quantitative measurement of the copies of the marker found in any sample. In other words, C_(t) values represent the presence of respective marker that the primer sets are designed to recognize. If the marker is missing in a sample, there should be no amplification in the Real Time-PCR reaction.

Alternatively, the C_(p) value may be utilized. A C_(p) value represents the cycle at which the increase of fluorescence is highest and where the logarithmic phase of a PCR begins. The LIGHTCYCLER® 480 Software calculates the second derivatives of entire amplification curves and determines where this value is at its maximum. By using the second-derivative algorithm, data obtained are more reliable and reproducible, even if fluorescence is relatively low.

The various and non-limiting embodiments of the PCR-based method detecting marker expression level as described herein may comprise one or more probes and/or primers. Generally, the probe or primer contains a sequence complementary to a sequence specific to a region of the nucleic acid of the marker gene. A sequence having less than 60% 70%, 80%, 90%, 95%, 99% or 100% identity to the identified gene sequence may also be used for probe or primer design if it is capable of binding to its complementary sequence of the desired target sequence in marker nucleic acid.

Some embodiments of the invention may include a method of comparing a marker in a sample relative to one or more control samples. A control may be any sample with a previously determined level of expression. A control may comprise material within the sample or material from sources other than the sample. Alternatively, the expression of a marker in a sample may be compared to a control that has a level of expression predetermined to signal or not signal a cellular or physiological characteristic. This level of expression may be derived from a single source of material including the sample itself or from a set of sources.

The sample in this method is preferably a biological sample from a subject. The term “sample” or “biological sample” is used in its broadest sense. Depending upon the embodiment of the invention, for example, a sample may comprise a bodily fluid including whole blood, serum, plasma, urine, saliva, cerebral spinal fluid, semen, vaginal fluid, pulmonary fluid, tears, perspiration, mucus and the like; an extract from a cell, chromosome, organelle, or membrane isolated from a cell; a cell; genomic DNA, RNA, or cDNA, in solution or bound to a substrate; a tissue; a tissue print, or any other material isolated in whole or in part from a living subject or organism. Biological samples may also include sections of tissues such as biopsy and autopsy samples, and frozen sections taken for histologic purposes such as blood, plasma, serum, sputum, stool, tears, mucus, hair, skin, and the like. Biological samples also include explants and primary and/or transformed cell cultures derived from patient tissues.

In some embodiments, sample or biological sample may include a bodily tissue, fluid, or any other specimen that may be obtained from a living organism that may comprise additional living organisms. By way of example only, in some embodiments, sample or biological sample may include a specimen from a first organism (e.g., a human) that may further comprise an additional organism (e.g., bacteria, including pathogenic or non-pathogenic/commensal bacteria, viruses, parasites, fungi, including pathogenic or non-pathogenic fungi, etc.). In some embodiments of the invention, the additional organism may be separately cultured after isolation of the sample to provide additional starting materials for downstream analyses. In some embodiments, the sample or biological sample may comprise a direct portion of the additional, non-human organism and the host organism (e.g., a biopsy or sputum sample that contains human cells and bacteria).

With respect to use of the sample or biological sample, embodiments of the claimed methodology provide improvements compared to conventional methodologies. Specifically, conventional methodologies of identifying and characterizing microorganisms include the need for morphological identification and culture growth. As such, conventional methodologies may take an extended period of time to identify the microorganism and may then require further time to identify whether the microorganism possesses and certain markers. Some embodiments of the invention can provide a user with information about any microorganisms present in a sample without the need for additional culturing because of the reliance of nucleic acid amplification and sequencing. In other words, direct extraction of nucleic acids coupled with amplification of the desired markers and downstream sequencing can reduce significantly the time required to obtain diagnostic and strain identifying information.

The invention may further comprise the step of sequencing the amplicon. Methods of sequencing include but need not be limited to any form of DNA sequencing including Sanger, next-generation sequencing, pyrosequencing, SOLiD sequencing, massively parallel sequencing, pooled, and barcoded DNA sequencing or any other sequencing method now known or yet to be disclosed.

In Sanger Sequencing, a single-stranded DNA template, a primer, a DNA polymerase, nucleotides and a label such as a radioactive label conjugated with the nucleotide base or a fluorescent label conjugated to the primer, and one chain terminator base comprising a dideoxynucleotide (ddATP, ddGTP, ddCTP, or ddTTP, are added to each of four reaction (one reaction for each of the chain terminator bases). The sequence may be determined by electrophoresis of the resulting strands. In dye terminator sequencing, each of the chain termination bases is labeled with a fluorescent label of a different wavelength that allows the sequencing to be performed in a single reaction.

In pyrosequencing, the addition of a base to a single-stranded template to be sequenced by a polymerase results in the release of a pyrophosphate upon nucleotide incorporation. An ATP sulfuryrlase enzyme converts pyrophosphate into ATP that in turn catalyzes the conversion of luciferin to oxyluciferin which results in the generation of visible light that is then detected by a camera or other sensor capable of capturing visible light.

In SOLiD sequencing, the molecule to be sequenced is fragmented and used to prepare a population of clonal magnetic beads (in which each bead is conjugated to a plurality of copies of a single fragment) with an adaptor sequence and alternatively a barcode sequence. The beads are bound to a glass surface. Sequencing is then performed through 2-base encoding.

In massively parallel sequencing, randomly fragmented targeted nucleic acids and/or amplicons are attached to a surface. The fragments/amplicons are extended and bridge amplified to create a flow cell with clusters, each with a plurality of copies of a single fragment sequence. The templates are sequenced by synthesizing the fragments in parallel. Bases are indicated by the release of a fluorescent dye correlating to the addition of the particular base to the fragment.

Nucleic acid sequences may be identified by the IUAPC letter code which is as follows: A—Adenine base; C—Cytosine base; G—guanine base; T or U—thymine or uracil base; I—inosine base. M—A or C; R—A or G; W—A or T; S—C or G; Y—C or T; K—G or T; V—A or C or G; H—A or C or T; D—A or G or T; B—C or G or T; N or X—A or C or G or T. Note that T or U may be used interchangeably depending on whether the nucleic acid is DNA or RNA. A sequence having less than 60%, 70%, 80%, 90%, 95%, 99% or 100% identity to the identifying sequence may still be encompassed by the invention if it is able of binding to its complimentary sequence and/or facilitating nucleic acid amplification of a desired target sequence. In some embodiments, as previously mentioned, the method may include the use of massively parallel sequencing, as detailed in U.S. Pat. Nos. 8,431,348 and 7,754,429, which are hereby incorporated by reference in their entirety.

Some embodiments of the invention comprise multiple steps and/or processes that are carried out to execute the universal tail indexing strategy to prepare amplicons corresponding to desired markers for sequencing. In some embodiments, one or more makers for a given sample or template can be selected, as described above. Some embodiments of the invention can be used in conjunction with an analysis of one or more markers (e.g., genes/alleles) associated with a particular phenotype (e.g., virulence).

After selection of the markers, marker-specific primers/oligonucleotides can be designed for the amplification of the markers to produce the desired amplicons, as detailed above. As is known in the art, a forward and a reverse marker-specific primer can be designed to amplify the marker from a nucleic acid sample. In some embodiments, the forward and reverse primers can be designed to produce an amplicon (e.g., some or all of the sequence of the marker) of a desired length. For example, the length of the amplicon may comprise approximately 50 base pairs (bp), 100 bp, 150 bp, 200 bp, 250 bp, 300 bp, 350 bp, 400 bp, 450 bp, 500 bp, 1,000 bp, or any size amplicon greater in size or therebetween.

As previously mentioned, some embodiments of the invention may include a multiplex PCR reaction. For example, marker-specific primers can be designed for multiple markers or multiple regions of the same marker such that multiple amplicons of between about 50 bp and 1,000 bp are being produced within a single PCR reaction vessel. In other words, the forward and reverse primers can be designed to function within a given set of temperature parameters such that more than one amplicon can be successfully amplified from a given template within a single PCR reaction mixture. As such, multiple amplicons can be prepared using the universal tail indexing strategy for sequencing preparation.

In some embodiments, the forward and reverse primers that have been designed for each of the markers can be modified to include a universal tail. For example, the universal tail sequences can be relatively or completely unique sequences of nucleotides that are coupled to the 5′ ends of some or all of the forward and reverse marker-specific primers. In some aspects, the universal tail sequences can be selected such that there is little to no overlap in sequence between portions of the markers that are being amplified and the universal tail sequences. Moreover, the universal tail sequences can comprise a length between ten and twenty nucleotides in length. In some embodiments, the universal tail sequences can be any other length, as desired by the user to meet the needs and requirements of the reaction. As such, the universal tail sequences can exhibit a relatively negligible impact on binding of the forward and reverse marker-specific primers to the template sequence to enable amplification. Moreover, as a result of being included on the 5′ end of the forward and reverse marker-specific primers, the universal tail sequences will form a portion of the resulting amplicons. In addition, in some aspects of the invention, the sequences selected for the universal tail sequences can be at least partially correlated with the chemical composition of the template nucleic acids. For example, in some aspects, the sequences selected for the universal tail sequences can be at least partially correlated with the G-C content of the organism from which the template is isolated.

In some aspects, some or all of the universal tail sequences can be at least partially unique. In some embodiments, each of the 5′ ends of all of the forward marker-specific primers within a given PCR assay mixture can comprise the same or a similar universal tail sequence (e.g., a first universal tail sequence or UT1). Similarly, each of the 5′ ends of all of the reverse marker-specific primers within the same PCR assay mixture can comprise a second universal tail sequence (UT2) that differs from the first universal tail sequence. As such, each respective sample from which a template sequence is used in the multiplex PCR assay will have two unique universal tail sequences. Accordingly, each forward and reverse marker-specific primer within a multiplex PCR mixture will include a unique universal tail sequence. For example, if the PCR includes 35 different samples, 35 universal tail sequences can be employed for the forward primers in each of the 35 unique reactions (i.e., not including technical replicates) and 35 universal tail sequences can be employed for the reverse primers in each of the 35 unique reactions (i.e., not including technical replicates). Overall, the forward and reverse marker-specific primers that each comprise the universal tail sequences can comprise a generally short length (e.g., 25-50 bp), which can facilitate simultaneous amplification of multiple targets in a single reaction.

In addition, some embodiments of the invention may comprise performing quantitative PCR to optimize the multiplex PCR assay. For example, after design of the forward and reverse marker-specific primers that each include a universal tail sequence, the contemplated multiplex PCR assays can be performed using quantitative PCR (e.g., using DNA as a template) to assess relative quantities of the amplicons produced. Accordingly, the sequence coverage of each amplicon is considered to be equal if the quantities of the amplicons produced by the multiplex quantitative PCR appear to be equal. If the quantities of the amplicons produced by the multiplex quantitative PCR do not appear to be equal, the forward and/or reverse marker-specific primers can be altered and re-optimized until adequate quantities of amplicons are produced.

After design and adequate optimization of the multiplex PCR assay comprising multiple forward and reverse marker-specific primers that each includes universal tail sequences, the multiplex PCR can be performed to obtain the amplicons associated with the above-described markers. In some embodiments, template that has been previously isolated from a sample can be used for the amplification of the amplicons. In some aspects, multiple PCR reaction replicates can be performed for each sample template and one or more control templates.

In some embodiments, after successful production of the amplicons during the multiplex PCR assay, the resulting amplicons can be further processed to provide sequencing-ready amplicons. For example, some embodiments of the invention may comprise an indexing extension step. In some aspects, the indexing extension step may comprise extending the optimized multiplex amplicons using a set of indexing and common primers that recognize the respective universal tail sequences used for the particular group of amplicons in a minimal cycle PCR assay (e.g., 5-10 total cycles). In particular, each multiplex set of amplicons to be sequenced can be extended with a different set of index oligonucleotides and common oligonucleotides that recognize UT1 and UT2, respectively. In some aspects, the index sequence of the index oligonucleotides can be custom designed to allow for the selection of an index sequence from potentially thousands of different index sequences.

After this step, the resulting products include a set of amplicons for each sample/template that comprise the same index and any necessary sequences that may be required for a particular sequencing platform (e.g., platform sequences associated with the ILLUMINA® Next Generation sequencing platform). Thereafter, the resulting extension-reaction products can be quantified, pooled, and sequenced using a desired platform. In some aspects, the inclusion of the universal tail sequences on the index and common primers can coincide with the use of genomic and index read primers in the mixture of sequencing primer reagents. For example, some embodiments of the invention are capable of pooling multiple amplicons with multiple indices in a single sequencing run to provide 40,000×-95,000× coverage across the amplicons. In other embodiments, the systems and methods associated with the invention can be configured to provide any level of sequencing coverage that is desirable to the user (e.g., higher or lower that the coverage levels discussed above). In some embodiments, after sequencing and generation of the sequence data, the resulting data can be demultiplexed and the sequence files can be aligned to the appropriate references sequences for subsequent sequence analyses.

Embodiments of the invention offer additional advantages relative to conventional systems. For example, some embodiments of the invention comprise the use of PCR before sequencing such that only limited amounts of starting material are necessary and the starting material need not be of high quality (e.g., genomic DNA, crude DNA extracts, single stranded DNA, RNA, cDNA, etc.). In contrast, many conventional sample preparation systems may require relatively large amounts of starting material of relatively high quality, which can limit the use of these systems. Moreover, the inclusion of non-desirable template materials can also interfere in one or more downstream processes in conventional systems and methods. For example, if an investigation is being conducted that focuses on one or more organisms that may be associated with another organism (e.g., bacteria associated with a human); the sampling of the target organism may result in template contamination from the host organism.

In particular, in some aspects, obtaining samples of pathogenic or commensal bacteria from, on, or within a human may also result in the collection of human tissue. As such, when isolating the template, human nucleic acids may contaminate the bacterial template. Some embodiments of the invention are configured such that the contaminating template (e.g., from a human) would not interfere with downstream processes, including sequencing. For example, some embodiments of the invention operate such that only a limited amount of starting template (e.g., 500 femtograms or greater) can be used. Moreover, some embodiments are also configured such that the starting material (e.g., template contaminated with foreign nucleic acids) can still produce the required amplicons for sequencing in the presence of more than a 1,000-fold excess of contaminating template with no discernible inhibition of the multiplex PCR.

In certain aspects, the present invention provides an assay that works with as little as about 1 pg, about 900 fg, about 800 fg, about 700 fg, about 600 fg, about 500 fg, about 400 fg, about 300 fg, about 200 fg, or about 100 fg of genomic DNA.

The following examples are given for purely illustrative and non-limiting purposes of the present invention.

EXAMPLES Example 1. Materials and Methods

Samples

Isolates for target identification and assay validation and DNA extracted from clinical specimens were acquired through collaborations with a large hospital reference laboratory that receives specimens from 10 system-wide medical centers in Arizona and from a high-volume private reference laboratory that receives specimens from regional inpatient, long-term care, and outpatient facilities. Isolates were identified with Vitek 2 (bioMérieux). Clinical specimen types included various respiratory specimens (nasal, ear, and throat swabs; sputum samples; tracheal aspirates; and bronchial alveolar lavage samples), urine, and wound swabs or tissue. DNA was extracted from isolates with the Qiagen DNeasy Blood and Tissue kit with additional lytic enzymes when appropriate. DNA was extracted from clinical specimens by NucliSENS easyMAG (bioMérieux, Durham, N.C.). DNA from healthy donor fecal samples was acquired from a family microbiome study; samples had been collected from members of seven families over multiple time points. DNA was extracted in accordance with the Earth Microbiome Project protocol (47). All of the samples were obtained from studies approved by the institutional review boards of the participating institutions.

Assay Target Identification and Assay Design.

FIG. 1 illustrates the methodologies and resources, also described below, utilized to amass a target library and develop several types of amplicon sequencing assays.

WGS, Single Nucleotide Polymorphism (SNP) Detection, and Phylogenetic Analysis

In-house genome libraries were prepared from 31 Klebsiella isolates and 6 non-Klebsiella isolates (to validate KlebSeq assays) with a 500-bp insert size with the KAPA Library Preparation kit and Standard PCR Library Amplification (Kapa Biosystems, Wilmington, Mass.) and sequenced on Illumina's GAIIx or MiSeq. Additional in-house genomes that we have previously described were also included and comprised 111 K. pneumoniae, 1 K. quasipneumoniae, and 5 K. variicola genomes. Public genome sequence data from 256 K. pneumoniae, 18 K. quasipneumoniae, and 13 K. variicola isolates were downloaded from the SRA database, and genome sequence data from 177 K. pneumoniae, 4 K. quasipneumoniae, and 11 K. variicola isolates were downloaded from the Assembly database, and all passed filters for high quality; i.e., assemblies and SRA data aligned with ≥80% of MGH 78578 or ≥88% of the strict core genome multilocus sequence typing (scgMLST) references (described below), SRA data at a ≥10× read depth.

NASP (48), developed for microbial genome analysis, was used to detect SNPs among genomes. In brief, reads were aligned with a reference genome, either one concatenated from scgMLST alleles (10) or MGH 78578 (GenBank accession no. CP000647) with Novoalign V3.04.04 (Novocraft Technologies, Selangor, Malaysia) and SNPs were called with GATK version 2.7-2 (49). Data filtered out included SNP loci with <10× coverage or with <90% consensus in any one sample, regions duplicated in the reference genome as identified by Nucmer, and SNP loci that were not present in all of the genomes in the data set. In NASP, results were output in a SNP matrix from a core genome common to all of the isolates in the analysis. Phylogenetic trees were generated from the NASP SNP matrices with MEGA 6.0 (50) and subsequently plotted by means of ITOL v2 or v3 (51).

Genomic Target Identification

To find whole gene targets for assay design, selected genomes were assembled with UGAP, which uses the SPAdes genome assembler, version 3.6, for this work (52). Assemblies were then run through LS-BSR (53), which generates a list of open reading frames (ORFs) that have high identity among target species genomes and that have low identity or are not present in nontarget genomes. Alleles of the candidate target ORFs were collected by BLAST, including alleles from nontarget genomes, if present. Lastly, alleles of candidate ORFs were aligned for assay design. Canonical SNPs (canSNPs) were identified from the SNP matrix generated by NASP. Sequence flanking each SNP was collected from the NASP reference genome.

AMR and Virulence Gene Target Collection

AMR and virulence gene sequences were identified and collected in several ways, including from the Klebsiella BIGSdb, public literature, and the NCBI. Public literature included a paper by Holt et al. (54) in which a species-wide analysis of K. pneumoniae genomes revealed several siderophore systems and other virulence factors associated more with infectious than with colonizing strains. AMR genes included the major ESBL and carbapenemase genes and plasmid-mediated quinolone resistance determinants, as well as the gyrA and parC chromosomal genes, several aminoglycoside resistance genes, trimethoprim-sulfamethoxazole, tetracycline, streptomycin, chloramphenicol, and fosfomycin resistance genes, and the recently discovered plasmid-mediated colistin resistance gene mcr-1. Virulence targets included several siderophore systems, for which multiple genes from each were used as assay targets; the regulator of the mucoid phenotype (an indicator of hypervirulence); the wzi gene for capsule typing, for which we used the previously published assay (55); and two genes highly associated with invasive infection, pK2044_00025 and pK2044_00325 (54). For genes that consist of highly diverse alleles, for example, blaCTX-M, qnrB, or dfrA, phylogenetic trees based on nucleotide sequences were generated in order to group similar alleles for assay design.

Assay Design and Validation

Gene-based target alleles were aligned in SeqMan (DNAStar, Madison, Wis.) to identify conserved regions for primer design, and assays were designed with guidance from RealTimeDesign (Biosearch Technologies, Petaluma, Calif.), or gene-based assays were generated with AlleleID (Premier Biosoft, Palo Alto, Calif.), which designs assays to capture alleles in an alignment rather than individual sequences. SNP assay primers were designed with RealTimeDesign, and primer sequences were checked for conservation in the NASP SNP matrix. Lastly, assays were run through BLAST to check for cross-reactivity with other relevant targets or species, including human. Universal tails were added to each primer sequence for library preparation as described below. The assays and their primer sequences are listed in Table 4.

Individual assays were screened across positive controls when they were accessible and screened across several isolate genomic DNAs (gDNAs) to test robustness. Additionally, multiplex PCR was validated by initial gene-specific PCR (described below), followed by PCR product dilution and then screening of individual assays by Sybr green-based quantitative PCR (qPCR). For this, 10-μl reaction mixtures of 1× Platinum SYBR green qPCR SuperMix (ThermoFisher Scientific, Waltham, Mass.), 200 nM forward and reverse primers of one assay, and 1 μl of diluted multiplex PCR product were run at 95° C. for initial denaturation for 4 min and then 40 cycles of 95° C. for 15 s and 60° C. for 1 min. Lastly, several panels of known isolate DNAs were screened by the amplicon sequencing method to test the sensitivity and specificity of the species and strain identification assays. AMR and virulence gene assays were validated by comparing amplicon sequencing results with WGS data.

Amplicon Library Preparation and Sequencing

Amplicon library preparation with universal tails was described in detail previously (56). Here, assays were combined into three assay pools for multiplex PCR (see Table 4), requiring three initial PCRs for each sample. The initial gene-specific PCR mixture comprised 12.5 μl of Kapa Multiplex PCR Mastermix (Kapa Biosystems, Wilmington, Mass.), 10 μl of primer mix (final concentration of 200 nM each), and 2.50 of template DNA from each sample and was denatured at 95° C. for 3 min; cycled 25 times at 95° C. for 15 s, 60° C. for 30 s, and 72° C. for 1 min 30 s; and subjected to a final extension at 72° C. for 1 min. The three multiplex PCR products from the same sample were combined, and PCR products were cleaned with 1× Agencourt AMPure XP beads (Beckman Coulter, Indianapolis, Ind.). A second PCR with the universal tail-specific primers added Illumina's sample-specific index and sequencing adapters. This PCR mixture comprised 12.5 μl of 2× Kapa HiFi HotStart Ready Mix (Kapa Biosystems), 400 nM each primer, and 1 to 10 μl of cleaned gene-specific PCR product and was denatured at 98° C. for 2 min; cycled 6 to 12 times at 98° C. for 30 s, 65° C. for 20 s, and 72° C. for 30 s; and subjected to a final extension at 72° C. for 30 s. Final PCR products were cleaned with 0.8× Agencourt AMPure XP beads (Beckman Coulter). Amplicon libraries from individual samples were quantified by qPCR with the Kapa Library Quantification kit (Kapa Biosystems). Samples were then pooled in equimolar concentrations for sequencing on the Illumina MiSeq platform with the 2×250 bp version 2 kit.

Analysis

Amplicon sequencing results were automatically analyzed with a newly developed amplicon sequencing analysis pipeline (ASAP) (45) that uses a JavaScript Object Notation (JSON) file customized to describe all of the assays in a multiplex. The information in the JSON file includes (i) a category for each assay (presence/absence, SNP, gene variant, or region of interest) that dictates how ASAP will report results and (ii) reference sequences for read mapping. In ASAP, amplicon sequence reads are first trimmed of adapter or readthrough sequences with Trimmomatic (57) and then mapped to the reference sequences with an aligner of choice. BAM alignment files are analyzed alongside the JSON file assay descriptions to determine the presence, percent identity, and breadth and depth of coverage of the reference and proportions of nucleotide polymorphisms for each amplicon. User-defined parameters for KlebSeq-prepared samples included the bowtie2 aligner (58) for all of the assays except for wzi, for which bwa (59) was chosen (because the reference sequence is shorter than the expected amplicon and reads need to be clipped to align [55]), and thresholds for determining results of screening included percent identities listed in Table 4, 80% breadth at 100× depth of coverage for isolate DNA, 80% at 20× (clinical specimens) or 10× (fecal specimens) depth, and a ≥10% proportion of polymorphism for informative SNP loci for complex-specimen DNA (meaning that at least 10% of the reads had to share a SNP state at a given locus for it to be reported). For WGS-prepared data, the parameters were bwa aligner (for clipping) and 80% breadth at 5× depth. The ASAP output includes an XML file containing details of the analysis of each assay target for each sample, which can be converted into a webpage interface by XSLT transformations. An example of a KlebSeq ASAP output for one sample is shown in FIG. 2. SeqMan NGEN (DNAStar, Madison, Wis.) and Tablet (60) were used to verify results.

Klebseq Validation

FIG. 3 and the following text outline the processes used to validate KlebSeq, and Table 4 shows the extent to which each assay was validated in multiplex. First, WGS data from 73 K. pneumoniae samples were analyzed for AMR genes, subjected to MLST via SRST2 (61) and species identification confirmation via phylogenetic analysis, and also analyzed by ASAP. gDNA from these same 73 samples plus gDNA from 149 other species was screened with KlebSeq. To validate KlebSeq's K. pneumoniae strain identification and AMR gene profiles in specimens, six isolates that had been cultured and identified in six of the specimens were sequenced and analyzed. Additionally, a PCR for MLST was performed with selected specimen DNAs by the protocol from the Klebsiella BIGSdb. DNA libraries from the PCR products were prepared for sequencing by the same protocol as for whole gDNA. Sequence data were run through SRST2 to determine the ST of the K. pneumoniae present in the specimen.

Example 2. Phylogenetic Analysis and canSNP Identification

With the Klebsiella scgMLST (10) assembly as a reference, SNPs among a diverse set of genomes from K. pneumoniae and genomes from newly defined K. quasipneumoniae (22 from the public databases and 1 from in-house isolates) and K. variicola (24 from the public databases and 5 from in-house isolates) were identified with NASP. canSNPs that differentiate K. quasipneumoniae and K. variicola from K. pneumoniae were selected for assay development.

With the reference genome MGH 78578 and 547 diverse K. pneumoniae genomes, NASP generated a SNP matrix from which canSNPs for each of the major clonal groups were selected for assay development. Clonal groups and locations of canSNPs identifying 21 clonal groups and 12 STs in the context of the K. pneumoniae species are illustrated in FIG. 4. Redundancy was intentionally included in identifying canSNPs for the most epidemic strains of K. pneumoniae, such as ST14, ST20, and strains in CG258, in order to increase sensitivity and confidence in positive results.

Example 3. Assay Development

The identification of genomic targets, canSNPs, and AMR and virulence genes and subsequent assay design resulted in two assays specific to K. pneumoniae (Kp-M1 and Kp-M2), one each for K. oxytoca (Koxy_UT), K. variicola (Kvari_UT), and K. quasipneumoniae (Kquasi_UT), 37 assays to identify clonal groups or lineages within clonal groups of K. pneumoniae, 76 AMR gene assays, and 15 virulence gene assays (see Table 4). The canSNP states for each strain identification assay are specific to that clonal group of K. pneumoniae, except in the case of CG35, where the amplicon must match the reference sequence 98%, allowing up to four additional SNPs, in order to be called CG35. Otherwise, identity thresholds for each strain identification assay are optional; they merely make the assays completely Klebsiella specific, regardless of the canSNP state.

Example 4. KlebSeq Validation on Isolate DNA

To validate the species and clonal group identification assays, gDNA from 73 K. pneumoniae isolates whose whole genomes were sequenced (4 of which were later identified as K. quasipneumoniae and K. variicola [see below]), 22 K. oxytoca isolates, and 157 other enteric opportunistic pathogen isolates, which included E. coli, Enterobacter aerogenes, E. amnigenus, E. cloacae, E. hormaechei, Enterococcus faecalis, E. faecium, an unknown Enterococcus species, Proteus mirabilis, Providencia stuartii, and Serratia marcescens, and 1 Acinetobacter baumannii isolate, were screened with KlebSeq. Sensitivity and specificity results of the species identification assays compared with clinical microbiological identification (Vitek 2) are in Table 1. With the redundancy built into the multiplex by including two assays, Kp-M1 and Kp-M2, that target two different K. pneumoniae species-specific genes (M1 and M2), 100% sensitivity is achieved. One isolate previously identified as K. pneumoniae was identified as K. quasipneumoniae, and two were identified as K. variicola. These isolates' whole genomes were added to the phylogenetic analysis of these three species that was previously run to find the species-specific canSNPs (see Materials and Methods). The K. quasipneumoniae and K. variicola genomes identified by our assay clustered with their respective species in the phylogeny (FIG. 5). Clinical methods do not currently distinguish among all three of these species, so assay sensitivity and specificity were not calculated for K. quasipneumoniae and K. variicola (Table 1).

TABLE 1 Results of KlebSeq species identification assays of genomic DNA from isolates whose whole genomes were also sequenced, DNA from specimens for which clinical culture results are known, and DNA from specimens with unknown content. DNA type (no, of samples) and species identified by clinical Total no. No. of isolates identified by amplicon sequencing assay^(b) methods or parameter^(a) screened Kp-M1 Kp-M2 Kp-M1 + Kp-M2 Kquasi_UT Kvari_UT Koxy_UT Isolate DNA (252) K. pneumoniae  69  68  67  69  0  0  0 K. quasipneumoniae  2  0  0  0  2  0  0 K. variicola  2  2  0  2  0  2  0 K. oxytoca  14  0  0  0  0  0  14 Nontarget species 149 Feb-88  0/88 Feb-88  0/155  0/155  0/135 % Sensitivity  99  97 100 100 100 100 % Specificity  98 100  98 100 100 100 Urine DNA (46) K. pneumoniae  16  14  15  16  2 (1 mix)^(c)  1 (mix)^(c)  0 K. oxytoca  6  1  1  1 (CG34)  0  0  6 Other species  24  1  1  1  0  0  0 Unknown  0  0  0  0  0  0  0 % Sensitivity  88  94 100 100 % Specificity  90  93  93 100 Wound DNA (40) K. pneumoniae  1  0  0  0  0  1  0 K. oxytoca  1  0  0  0  0  0  1 Other species  31  0  0  0  0  0  0 Unknown  7  1  1  1 (CG29)  0  0  1 % Sensitivity  0  0  0 100 % Specificity 100 100 100 100 Respiratory specimen DNA (87) K. pneumoniae  6  6  6  6  0  0  0 K. oxytoca  1  0  0  0  0  0  1 Other species  77  7 (1 ST258)  5  7 (2 CG36,  0  0  1 1 CG37) Unknown  3  0  0  0  0  0  0 % Sensitivity 100 100 100 100 % Specificity  91  94  91  99 Fecal specimen DNA (89)  89  9  5  9  1 (mix)^(c)  3 (2 mix)^(c)  13 All specimens (isolates not included) (262) K. pneumoniae  23  20  21  22  2  2  0 K. oxytoca  8  1  1  1  0  0  8 Other species 132  8  6  8  0  0  1 Unknown  99  10  6  10  1  3  14 % Sensitivity  87  91  96 100 % Specificity  94  95  94  99 ^(a) K. quasipneumoniae is not distinguished from K. pneumoniae by the clinical identification method used (Vitek 2). ^(b)Kp-M1 and Kp-M2 are K. pneumoniae species identification assays that detect targets M1 and M2 in the K. pneumoniae genome. Kquasi_UT, Kvari_UT, and Koxy_UT are K. quasipneumoniae-, K. variicola-, and K. oxytoca-specific assays, respectively. ^(c)These species were found as mixtures with K. pneumoniae on the basis of a proportion (>10%) of the sequencing reads containing the species-defining SNP.

Table 2 shows the KlebSeq results of the K. pneumoniae clonal group identification and capsule typing assays of isolate DNA. Each isolate's strain type was correctly captured by the appropriate assays or not captured in cases where no assay was designed for that clonal group. Included in Table 2 are results from partial sequencing of the wzi gene for capsule typing. This gave surprisingly clear results, given that approximately 75 bp of the informative region are missing from our sequence output, as the PCR amplicon is approximately 580 bp (55), which is too long to cover with the Illumina version 2 sequencing chemistry. However, full capsule typing by wzi sequencing would be possible with longer-read chemistry (i.e., Illumina version 3 chemistry, for 600-bp reads). Results from screening of nontarget organisms showed that several of the K. pneumoniae clonal group assays amplified DNA from other organisms, as expected. An identity threshold can be applied (see Table 4); however, all of the SNP states that define a particular clonal group are specific to that clonal group, except for CG35, so the identity threshold is optional except for this assay. Sequence analysis by ASAP reports when a clonal group is present only if the defining canSNP state is present and reports nothing if it is not.

TABLE 2 Isolates used for assay validation and results of strain typing by amplicon sequencing^(a) ASAP strain Capsule typing Isolate No. of typing assay result(s) by partial ST isolates result(s) wzi sequencing^(b) ST11 3 CG258, CG258 without 395 wzi-39 or -75, wzi-74, not typeable ST14 5 CG14, ST14, inner ST14 All wzi-2 ST14 1 CG14 wzi-16 SLVd ST15 2 CG14, ST15 All wzi-24 or -45 ST20 2 CG20, ST20 wzi-84, wzi-118 ST23 8 ST23 wzi-1 ST34, 2 CG34 wzi-114, wzi-12 ST34 SLV ST36 2 CG36 All wzi-27 or -79 ST37 2 CG37 wzi-50, wzi-39 or -75 ST39 1 No group wzi-2 ST42 2 CG42, inner CG42 All wzi-29 ST43 1 CG43 wzi-30 ST45 1 CG45 wzi-133 ST65 1 CG25 wzi-72 ST101 2 CG43 wzi-29, wzi-137 ST107 1 No group wzi-74 ST111 1 CG111 wzi-63 ST147 1 CG392 wzi-64 ST152 1 CG105 wzi-150 ST228 1 CG34 wzi-116c ST234 1 No group wzi-114 ST249 2 No group All wzi-128 ST258, no 6 CG258, CG258 without All wzi-154 clade ST395, ST258 ST258, 3 CG258, CG258 without All wzi-29 clade 1 ST395, ST258, clade 1 ST258, 2 CG258, CG258 without All wzi-154 clade 2 ST395, ST258, clade 2 ST277 1 No group wzi-97 or -185 ST334 1 K. quasipneumoniae wzi-68 ST340 2 CG258, CG258 without wzi-50, wzi-173 ST395, ST340 ST376 1 CG42, inner CG42 wzi-2 ST380 1 ST380 wzi-203 ST437 1 CG258, CG258 without 395, wzi-109 ST437 ST636 1 No group wzi-155 ST719 1 No group wzi-192 ST776 1 No group wzi-39^(c) or -75^(c) or -193^(c) ST833 1 CG258, CG258 without 395 wzi-50 ST978 1 K. quasipneumoniae wzi-212^(c) ST1401 1 No group wzi-96 ST82 2 No group All wzi-128 ST260 1 No group wzi-1 ST360 1 K. variicola wzi-53 SLV ST427 1 No group wzi-64 SLV ST513 1 No group wzi-87 SLV ST815 1 No group wzi-114^(c) SLV ST244 1 No group wzi-162^(c) SLV ST2006 1 K. variicola wzi-227 ST2055 1 No group wzi-14 ^(a)Table 5 lists the genome accession numbers of the isolates. ^(b)The Illumina version 2 chemistry used provides approximately 500 bp of sequence data. The amplicon size for the wzi assay is approximately 580 bp (55). ^(c)The wzi allele represents the best match; one or more SNPs were present. ^(d)SLV, single-locus variant.

AMR gene detection by amplicon sequencing was validated by comparing ASAP results with AMR gene screening of WGS with SRST2 (61) and with ASAP. Results showed an almost perfect correlation between KlebSeq ASAP and WGS ASAP, indicating that the KlebSeq PCRs are performing well. There were a few discrepancies with SRST2, which reported uncertainty (SNPs or low-coverage indicators) for most of the discrepancies. Some discrepancies were in the presence of the dfrA gene. This group of genes is very diverse, so it may be that KlebSeq does not capture the full repertoire of dfrA genes. Virulence gene detection was validated by comparing ASAP results from WGS data with those from amplicon sequence data, and results showed concordance. In addition, by targeting multiple genes that are part of the same virulence factors (i.e., siderophore systems), sensitivity and confidence in results were increased.

These results also confirm that KlebSeq is applicable to pure isolates as well as complex specimens. Screening of isolate DNA has the added benefit of traceability of the AMR and virulence genes, which are often carried on mobile genetic elements, to their host. Isolate screening could be used for surveillance and other purposes for identifying or characterizing Klebsiella.

Example 5. Specimen Sample Results

KlebSeq was run on DNA from 87 respiratory specimens, 46 urine specimens, 40 wound specimens, and 89 fecal samples from healthy. Sensitivity and specificity results of the species identification assays compared with those of clinical microbiological methods are shown in Table 1. In most cases, sensitivity was high, except in the wound specimens, where the one sample clinically identified as K. pneumoniae was identified as K. variicola. Some sensitivity and specificity calculations may be misleadingly low, as amplicon sequencing identified some samples as containing K. pneumoniae that actually contained K. quasipneumoniae or K. variicola, and several as containing Klebsiella that went undetected by clinical microbiological methods, including several in which clonal groups were also detected. In the healthy donor specimens, K. oxytoca (n=13) was more prevalent than K. pneumoniae (n=9). Sequencing read depth was low in some samples; this may have been due to dilution of the DNA samples before screening, as each was diluted 1:10 in water.

Important Klebsiella clonal groups were detected in multiple specimens. In the 17 urine samples positive for K. pneumoniae, clonal identifications included CG34, ST20, CG45, CG392 (which includes the NDM producer ST147 [62], though this sample was negative for blaNDM), ST133, and CG111. In wounds, the only sample K. pneumoniae positive by KlebSeq was CG29. From respiratory specimens, groups CG37 (n=2), ST134 (n=1), ST258 (n=2), CG36 (n=3), and inner ST14 (n=1) were identified. Interestingly, several clonal groups were identified in the healthy donor fecal specimens as well. In the nine K. pneumoniae-positive samples, the groups included ST20, CG37, and CG76, which are all members of multidrug-resistant outbreak strain types (11, 12, 15), along with ST133 and ST380. ST380 is associated with a K2 capsule type and hypervirulence and causes pyogenic liver abscesses in healthy people, especially those of Asian ethnicity (63). Many Asians are colonized by hypervirulent K1 or K2 capsule strain types; however, the level of risk of subsequent liver infection is unknown (63). For this sample, no wzi gene sequence was obtained; thus, the capsule type is unknown. A majority of the K. pneumoniae isolates in our samples did not fall into the major clonal groups targeted by KlebSeq. These strains probably all belong to lesser-known clonal groups, as more studies are showing that many K. pneumoniae infections are caused by nonepidemic, sporadic strains (64, 65).

Numerous and variable AMR genes were detected in the specimens, including different variants of the same gene that confer different phenotypes. With sequence-based information, we demonstrate that seven of the K. pneumoniae had key mutations in the gyrA gene known to confer resistance to fluoroquinolones. Additionally, several samples contained the aac(6′)-Ib gene for aminoglycoside resistance, and five of those contained the sequence variant aac(6′)-Ib-cr for fluoroquinolone resistance; mixtures of these two genes were also detected. Many of the infection specimens (nonhealthy donor specimens), both positive and negative for K. pneumoniae, were positive for other aminoglycoside resistance genes, as well as tetracycline, trimethoprim-sulfamethoxazole, streptomycin, fosfomycin, and chloramphenicol resistance genes. A few contained plasmid-mediated quinolone resistance genes. Several samples, especially the respiratory specimens, were also positive for KPC and CTX-M group 1 and 9 genes. Most of the healthy donor specimens were positive for trimethoprim-sulfamethoxazole resistance genes, and many were positive for streptomycin, aminoglycoside, tetracycline, and fosfomycin resistance genes. Interestingly, 39 of the 89 were positive for npmA, a relatively recently described pan-aminoglycoside resistance gene (66). These specimens were the only samples positive for this gene. Three specimens contained plasmid-mediated quinolone resistance genes. Fortunately, none were found to contain ESBL or carbapenemase genes. No complex specimens in this study were positive for genes encoding the important carbapenemases OXA-48, VIM, and NDM, and none were positive for the plasmid-mediated colistin resistance gene mcr-1.

These sets of samples did not appear to contain especially virulent strains of K. pneumoniae. The yersiniabactin siderophore genes were, by far, the most prevalent of the virulence genes tested, although positive samples made up less than half of the K. pneumoniae-positive samples. No specimens were positive for rmpA, the regulator of mucoid phenotype gene, including the ST380-containing sample, and few were positive for the salmochelin siderophore genes, which are associated with invasive K. pneumoniae infection (54). One respiratory specimen that contained an ST14 strain was positive for a K2 capsule type by partial wzi sequencing. K2 strains of K. pneumoniae are associated with hypermucoviscosity and hypervirulence, as previously mentioned. However, this respiratory sample was not positive for rmpA, and a recent study proposed that the presence of multiple siderophore system genes (linked to K1 or K2 capsule genes) explains hypervirulence rather than capsule type (54). In our data, K. pneumoniae-containing samples were positive for multiple siderophores or other virulence-associated genes only 15% of the time. Sequencing of wzi revealed a variety of capsule types and cases in which the same clonal groups had different wzi genotypes and in which they had the same genotype. This character would help identify or rule out a transmission event when patients carrying the same strain are found.

On an interesting note, in the healthy donor fecal samples collected from members of the same families over time, out of the nine K. pneumoniae-positive samples, only two came from the same person over time. The characterization assays suggest that the same strain of K. pneumoniae was present at both time points. K. pneumoniae-positive samples were found in multiple members of two of the seven families. In one of these families, the positive members carried strains different from one another, and in the other, it appears that two members had CG37 isolates with the same capsule type. The sample set is too small to draw conclusions from these data; however, the data raise interesting questions about community K. pneumoniae carriage.

Example 6. Validation of KlebSeq Strain Identification in Specimens

Table 3 shows MLST results from WGS data of six isolates cultured from specimens run on KlebSeq and from MLST PCR and sequencing of 11 specimens run on KlebSeq. In each case, KlebSeq appears to have identified the correct strain. Two isolates for which no strain type was identified by KlebSeq have novel STs. Sample TG75900 was identified as K. quasipneumoniae by KlebSeq and typed as ST196 on the basis of whole-genome data. This genome was added to the phylogeny of the three species and clustered with K. quasipneumoniae (FIG. 5). MLST of the specimen DNA did not yield results for all of the MLST loci of all 11 samples, which is to be expected given the complexity of the specimen DNA sample. In cases where only partial data were retrieved, at least three alleles from each match the strain identified by KlebSeq.

TABLE 3 Results of KlebSeq strain identification validation by MLST of isolates cultured from specimens tested by KlebSeq and MLST of specimens tested by KlebSeq KlebSeq No. of loci identification of retrieved from Sample Type original specimen sequence data ST by MLST TG69923 Isolate CG29 7 Novel; DLV^(a) of ST29 TG75899 Isolate CG392 7 ST392 TG75900 Isolate K. quasipneumoniae 7 ST196 TG75901 Isolate ST133 7 Novel; SLV^(b) of ST133 TG75902 Isolate No strain ID 7 Novel; DLV of ST248 TG75911 Isolate Mixture of 7 Novel; TLV^(c) of K. pneumoniae ST633 with no strain ID and K. variicola TG69737 Urine CG34 7 Novel; 4 alleles match ST34 TG69766 Urine CG45 6 6 alleles match ST45 TG69776 Urine CG111 7 Novel; DLV of ST111 TG69861 Respiratory No strain ID 7 Novel; SLV of ST393 TG69865 Respiratory ST134 6 5 alleles match ST134 TG69871 Respiratory CG37 3 3 alleles match ST37 TG69883 Respiratory ST258 7 Novel; 3 alleles match ST258 TG73885 Respiratory CG36 7 Novel; 3 alleles match ST36 TG73911 Respiratory Mixture of 6 4 alleles match K. pneumoniae ST36 with no strain ID and CG36 TG73916 Respiratory Inner ST14 7 Novel; 4 alleles match ST14 TG74003 Respiratory Mixture of 7 Novel; DLV of K. pneumoniae ST461 no strain ID and CG36 ^(a)DLV, double-locus variant. ^(b)SLV, single-locus variant. ^(c)TLV, triple-locus variant.

In the United States, HAI is estimated to affect 1 in 25 hospital patients, totaling hundreds of thousands of patients, with significant mortality (2). HAIs have a significant impact on health care costs; a 2009 CDC report estimated upwards of $45 billion in annual additional cost (67). Infections with AMR organisms cause significantly higher mortality rates, significantly more intensive care unit (ICU) admissions, and significant excess costs, including hospitalization, medical care, and antimicrobial therapy, than do infections with susceptible strains (5, 68). HAI prevention measures, although costly in and of themselves (69), have the potential to save thousands of lives and billions of dollars (67). Periodic patient screening and isolation of AMR organism carriers have proven successful in controlling transmission and outbreaks in several hospitals (31, 34-37). Use of a highly informative screening and surveillance tool such as KlebSeq has cost-effective and life-saving potential.

Early detection of colonization of health care patients by K. pneumoniae, especially multidrug-resistant K. pneumoniae, would allow health care staff to make more informed patient management decisions. In outbreak situations, rapid identification of transmissions before subsequent infections would allow for proactive measures to curb an outbreak. In nonoutbreak situations, identification of particular strains and AMR genes would help to assess the risk of K. pneumoniae carriage to the host patient, as well as to other patients, as some strains are more closely associated with adverse outcomes (e.g., outbreaks, HAI, AMR, and treatment failure) than others (7-13, 70). Although our understanding of many Klebsiella virulence factors is limited, identification of virulence genes gains us understanding of the correlations between particular virulence factors and the risk of disease (54). Additionally, many K. pneumoniae infections, including HAIs and non-multidrug-resistant infections, are caused by nonepidemic, lesser-known strain types (64, 65). Classifying the K. pneumoniae isolate in each patient sample would help an institution to decide when and which intervention procedures should be enacted and also to understand more about transmission dynamics and local strain type circulation.

KlebSeq has several characteristics that make it attractive as a health care screening approach. With a single assay, enough information is garnered about a patient's Klebsiella carriage status to contribute greatly to patient management and to infection control decisions. Indexing samples by means of the universal tail during sample preparation allows the characterization of a large number of specimens in one run, minimizing sequencing costs per specimen and allowing for high-throughput screening of hundreds of patient samples simultaneously at a cost of tens of dollars per patient. KlebSeq uses DNA extracted directly from a specimen, so targets from entire populations of a species are analyzed to capture different strains in the same sample, which can be numerous (71, 72). If culture-based methods are used for screening, different strains are missed when one genotype (i.e., colony) is chosen for characterization, and the resulting information is limited. Additionally, culture-based methods can miss “silent” multidrug-resistant K. pneumoniae strains that test negative for carbapenemases in vitro (16), and if used for high-throughput screening, they can be laborious, time-consuming, costly, and subjective (31, 38). If screening of large numbers of patients by amplicon sequencing is cost-prohibitive, it can be limited to the highest-risk groups of patients, i.e., long-term care facility patients (31, 73), travelers returning from regions where Klebsiella carriage is endemic (74, 75), ICU patients (28), patients with previous K. pneumoniae carriage (75-77), patients who have shared a room with a known carrier (78) or case contacts of carriers (79), those who have recently taken antibiotics (80, 81), or patients on mechanical ventilation or enteral feeds or who have had prior Clostridium difficile infections (82). Additionally, using ASAP makes the analysis in KlebSeq streamlined and results are easily interpretable. Lastly, the amplicon sequencing and ASAP package is customizable and updateable (45). Individual assays can be added or removed, adding only the cost of new primers.

The results we present here show that KlebSeq is effective with DNA from numerous sample types, including pure organism culture, or complex, multiorganism samples and swab samples with low-level microbial DNA in a presumably high human DNA background without culture methods. In addition to clinically important clonal lineages of K. pneumoniae, KlebSeq also reliably distinguishes among the Klebsiella species, two of which, K. quasipneumoniae and K. variicola, are continuously misidentified as K. pneumoniae (as exemplified in our study) and cause invasive disease (83, 84). Additionally, we highlight several instances where culture methods failed to produce a positive K. pneumoniae result, including one sample that contained the critical ST258 strain. The sensitivity of KlebSeq is superior to that of culture-based methods for complex specimens, lowering the risk of false negatives in patient screening. We identified dozens of AMR and virulence genes within individual samples, demonstrating the additional function of profiling for clinically important characteristics, and were able to distinguish minor genotype differences that confer different phenotypes, such as the gyrA gene, aac(6′)-Ib versus aac(6′)-Ib-cr, and the wzi gene.

Notably, our data show that healthy individuals may carry clinically important strains of K. pneumoniae and frequently K. oxytoca, as well as many AMR genes and siderophore virulence systems. For our purposes, these healthy donor fecal DNA samples were used to validate the use of our amplicon sequencing approach with highly complex fecal metagenome samples. Much more study is needed to elucidate the implications of healthy host carriage of known pathogenic strains of K. pneumoniae and their virulence factors. Furthermore, the fact that we observed carriage of the hypervirulence-associated ST380 strain from a healthy person and the hypervirulence-associated K2 capsule type in an ST14 strain from a respiratory infection lends credence to the idea that we need much more information about K. pneumoniae carriage strains to be able to draw conclusions about these associations. Aside from these important observations, other observations from these data raise questions about the dynamics of K. pneumoniae carriage and microbiome sharing. The fact that there were not more cases of positive results from the same person at multiple rather than single time points is interesting. This could be due to intermittent shedding of K. pneumoniae in feces, intermittent colonization by K. pneumoniae, or heterogeneity in the sample itself, underrepresenting the full microbial community when a small sample is taken; this observation further warrants periodic rather than one-time screening of patients at risk. Of the two instances where two family members carried K. pneumoniae, each tells a different story about microbiome sharing. An amplicon sequencing-based diagnostic approach would facilitate longitudinal patient screening because of ease of use and limited costs.

Among the many pathogens encountered in health care institutions, we focus only on Klebsiella because of its high priority in public health and the high risk of CPE establishment in a facility. Additionally, although many other HAI agents cause devastating and costly infections, directing a complex assay such as KlebSeq at a subset of those agents greatly simplifies the validation process and speeds the availability of assay results (especially in the case of validation for FDA approval [85]). KlebSeq is an important step toward a comprehensive yet accessible tool for all pathogen identification and characterization. Metagenomic analysis is attractive in its breadth of coverage capabilities, but its current costs and complexities are prohibitive. Amplicon assays targeting the other ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens and more AMR determinants could relatively easily be added to the tool described here, with a step-by-step validation process. We have not found the limit of the multiplexing capacity. (We run three multiplexed PCRs merely because the PCR volume limits the number of primers that can be added; future assays will utilize primers at a higher concentration to test the multiplexing limit.) The multiplexing limit is also presumably dependent on the number and sizes of targets that are present in a sample, potentially exhausting the polymerase or sequencing space. These pieces are unpredictable for specimens of unknown content. Lastly, our report serves as evidence in favor of the concept that highly multiplexed amplicon sequencing is one good answer to the call for early detection tools in infection control.

KlebSeq is designed for screening and periodic surveillance in high-risk situations with a rule-in/rule-out determination of the possibility of transmission events and through identification of high-risk multidrug-resistant or epidemic strains of Klebsiella. For these purposes, KlebSeq is ideal. The specimen types used for validation could be considered a limitation, as we did not test rectal swabs, a specimen type commonly used for CPE surveillance. However, we show that KlebSeq works with different swab types and fecal specimens, which addresses the challenges of detection in rectal swabs. The turnaround time from sample collection to result is dependent only on current technology (not organism culture), and we recently conducted a proof-of-concept study of a 24-h sample-to-answer test with different targets (data not shown). This test was done on an Illumina MiSeq with only 60 cycles. Other platforms and upcoming technology may allow this turnaround time to be decreased even further.

Rapid amplicon sequencing with automated analysis and reporting is a promising response to the need for constant surveillance for highly transmissible or highly drug-resistant pathogens. Our model system, directed at Klebsiella, can easily be adapted to multiple other pathogens and to different purposes, such as environmental sampling and community host screening and, as smaller, more on-demand next-generation systems become available, to diagnostics and individual patient monitoring. The targeted, highly multiplexed nature of amplicon sequencing and the ability to interpret the data instantly make it an applicable tool for health care facility surveillance. As these technologies are adopted, considerable coordination within the health care facility is paramount to the success of infection and outbreak prevention, with the integration of isolation and barrier precautions, excellent communication, and good stewardship. Nevertheless, several institutions have shown that the combination of surveillance and systematic response reduces outbreaks and multidrug-resistant infections (31, 33-37).

TABLE 4 KlebSeq assay information Threshold of Example Validation identity to isolate used method reference where Multi- for WGS when no appropriate plex Primer Sequence SEQ Amplicon validation isolate (Maximum number Assay Assay Name Assay type Primer Name without Universal Tail^(a) ID NO: length of assay available of SNPs allowed) Pool Species Identification Assays Kp-M1_UT presence/ Kp_M1_UT1_F CGTTCCTCACCGTAGTGG   1 321 See Table 1 97%(10) 1 absence Kp_M1_UT1_R TCCAGCGTGACATAATCGG   2 94%(20) to include identification of K. variicola and K. quasipneumoniae Kp-M2_UT presence/ Kp_M2_UT1_F TGCCTATCGCCACTTTATTGA   3 366 See Table 1 97%(15) 1 absence Kp_M2_UT1_R CGGTCGTTAATCGCCTTCT   4 Koxy_UT presence/ Koxy_UT_F CCGTCGCCGTATTACTGAT   5 362 See Table 1 1 absence Koxy_UT_R TCTCTACAACACGCTACCCTA   6 Kvari_UT SNP (T43 to Kvari_UT_F TCAGCTATCGCCTGGAGTGCTA   7 287 See Table 4, 91%(26) 3 G, T67 to C, FIG. 3 C91 to T, G126 to A, G143 to T, T181 to C, G184 to T, A220 to G, A235 to G) Kvari_UT_R CTGCTCCTGGCCGACAAAC   8 Kquasi_UT SNP (A39 to Kquasi_UT_F GCCATAATGCAGCCTTTGC   9 187 See Table 4, 92%(15) 3 G, A51 to G, FIG. 3 G63 to A, A78 to C, G82 to C, T147 to C) Kquasi_UT_R ATCGCGTGAACGTCAGCTTCT  10 Clonal Group Identification Assays ST3_UT SNP (C25 to T) ST3_UT_F GCAGCCGTACAGACCGA  11 237 Sequence KlebSeq on 98%(5); also identifies 3 type not non-ST3 K. variicola and available K. pneumoniae K. quasipneumoniae ST3_UT_R CYATTCGCCAGCAGGACTA  12 CG14_UT SNP (G42 to A) CG14_UT_F GGGATCGASTTCACGTCCAC  13 271 See Table 4 94%(17) 3 CG14_UT_R ACGCCGAGGGACARGAGM  14 ST14_UT SNP (T33 to A) ST14_UT_F GCAGATTTAACCGAGCTGGTCT  15 205 See Table 4 98%(5) ST14_UT_R AGAGCGATGGCGAAGAGA  16 innerST14_UT SNP (G37 to A) innerST14_UT_F CGACAACCGCTTCGCTACC  17 273 See Table 4 96.5%(10) 3 innerST14_UT_R AGYACCGGGCGCAGATTG  18 ST15_UT SNP (C26 to T) ST15_UT_F GMACGCCGACGTCATYCT  19 271 See Table 4 93.5%(18) 3 ST15_UT_R CAGTGCTTGCATAGTGTCCTCTT  20 CG20_UT SNP (T37 to C) CG20_UT_F CGGTGGTGTTTGTCTGAACG  21 144 See Table 4 98%(3) 3 CG20_UT_R CAGGTGCGGATCTTGTCAATG  22 ST20_UT SNP (G35 to A) ST20_UT_F TCTTTGATCTTGTCCGGGTTGA  23 240 See Table 4 98%(5); also identifies 3 K. variicola and K. quasipneumoniae ST20_UT_R CCTCGGCGATATGGACTTCA  24 ST23_UT SNP (T36 to A) ST23_UT_F GCTRCCGTTGACCTTTATTGC  25 247 See Table 4 97%(8); also identifies 3 K. variicola and K. quasipneumoniae ST23_UT_R GCCGAAGCGTTCATAGAAATCC  26 CG25_UT SNP (C57 to T) CG25_UT_F GGCATTGGCGTCAATAAAGC  27 266 See Table 4 96%(11) 3 CG25_UT_R ATAGCCGCCAGACGAATTACCA  28 CG29_UT SNP (C30 to G) CG29_UT_F TCGACAACATCGTCGTCTTTC  29 259 See Table 4 98%(6) 3 CG29_UT_R TGCTGCACAGCACTCGTAAG  30 CG34_UT SNP (C36 to T) CG34_UT_F GACGATGTYGATGTGGCGATT  31 293 See Table 4 96%(12) 3 CG34_UT_R ACGCCCTGCCCGTGAATG  32 CG35_UT^(b) SNP (C34 to T) CG35_UT_F GTCGTCTGGTTCGGTCATTC  33 247 Sequence type KlebSeq on 98%(5) 3 not available non-CG35 K. pneumoniae CG35_UT_R GGTGTACAGCGAGGTCATAAAG  34 CG36_UT2 SNP (A31 to G) CG36_UT2_F GGCAGGCATGGAGCGTGT  35 245 See Table 4 97%(8); also identifies 3 K. variicola and K. quasipneumoniae CG36_UT2_R GCTTCGGCAGTAAACCGTAA  36 CG37_UT SNP (G40 to A) CG37_UT_F CCCGTTGGCCATCGTATGTC  37 250 See Table 4 96.5%(9) 3 CG37_UT_R GAGCGCATAGAAGTGACCATTC  38 CG42_UT SNP (C40 to A) CG42_UT_F CTCYAGCACGATGTCGTAAGG  39 248 See Table 4 97.5%(7) 3 CG42_UT_R GCGAGCATCGYGAGATTAGYG  40 innerCG42_ SNP (C41 to T) innerCG42_UT_F GCCCAAAGCATGGTCTATGAAC  41 248 See Table 4 96.5%(9) 3 UT innerCG42_UT_R CGCACGTCGGTTATTTGGTTG  42 CG43_UT SNP (T24 to C) CG101_UT_F GGRCCCAGCTATGTGC  43 264 See Table 4 96%(11); also identifies 3 K. variicola and K. quasipneumoniae CG101_UT_R CCACCATTCRATGCTTGCTTT  44 CG45_UT SNP (C27 to A) CG45_UT_F ACCGGCTCGTCGCCTTTC  45 228 See Table 4 96.5%(8) 3 CG45_UT_R TCACACCAGCCCATATACCA  46 CG48_UT SNP (T34 to A) CG48_UT_F GCTTCGCATTCTGGTAGCTGT  47 164 Sequence type KlebSeq on 97%(5); also identifies 3 not available non-CG48 K. variicola and K. pneumoniae K. quasipneumoniae CG48_UT_R CAACTCGGCRCTGTTCGT  48 CG76_UT SNP (G29 to A) CG76_UT_F TAGCCGCTCTTGTTGATGGA  49 236 Sequence type KlebSeq on 98%(5); also identifies 3 not available non-CG76 K. variicola and K. pneumoniae K. quasipneumoniae CG76_UT_R ACGCTGTGGACGCAGTA  50 CG86_UT SNP (C31 to T) CG86_UT_F ATACCCGGCGGAAGAYCT  51 240 Sequence type KlebSeq on 97.5%(6) 3 not available non-CG86 K. pneumoniae CG86_UT_R AGGGCCAGCATCGCTTTCAG  52 CG105_UT SNP (C27 to T) CG105_UT_F CAGCCAGGACGCTTTCGTTAG  53 258 See Table 4 96.5%(10) 3 CG105_UT_R TCGGCGTTGAGGTTRCT  54 CG111_UT SNP (C41 to T) CG111_UT_F CCAGCAACTGCGCTTTGTC  55 270 See Table 4 96%(11) 3 CG111_UT_R CGTCTGGAGCATGGAAGATGA  56 ST133_UT SNP (C40 to T) ST133_UT_F CGTTCTCAGCAGTTCGATTTCA  57 266 See Table 3 90%(28) 3 TCT ST133_UT_R CGCCGATAAGCAGTCGCT  58 ST134_UT SNP (G34 to T) ST134_UT_F CCGATGGCGACAAATAAACCA  59 263 Sequence type Specimen 97%(8) 3 not available MLST ST134_UT_R GCAGTGGAAGAGGCTCTGTA  60 KlebSeq on non-ST134 K. pneumoniae CG220_UT SNP (G31 to A) CG220_UT_F CAACCCGGCGCACTTTC  61 253 Sequence type KlebSeq on 98%(6); also identifies 3 not available non-CG220 K. variicola and K. pneumoniae K. quasipneumoniae CG220_UT_R CGCGTCCAGACGATATCTTTG  62 CG258_UT SNP (G45 to A) CG258_UT_F TTRACAGAATGGCAGAGAAGAA  63 234 See Table 4 98%(5) 3 AGG CG258_UT_R GTGGCGGCGTTTACAAATCAG  64 CG258wo395_ SNP (T42 to G) CG258wo395_ GAGCTGACCGAAGAGTTCATCA  65 259 See Table 4 98%(6); also identifies 3 UT UT_F K. variicola and K. quasipneumoniae CG258wo395_ GCAGTTCCAGAGCCTGTTTC  66 UT_R ST258_UT1^(c) SNP (T25 to C) ST258_UT1_F ATGGTGGTGCGCCAGTG  67 120 See Table 4 95%(6); also identifies 3 K. variicola and K. quasipneumoniae ST258_UT1_R GCTGACCGAGACGTTGTC  68  ST258_UT2 SNP (T30 to A) ST258_UT2_F TCAGTTTGCCAGTCTCGGTTT  69 238 See Table 4 97%(9) 3 ST258_UT2_R GCGTCTGGCGTAAGAGGTA  70 ST258clade1_ SNP (C35 to A) ST258clade1_ GATCAGATCCAACGGGCAGAA  71 234 See Table 4 96.5%(9) 3 UT UT_F G ST258clade1_ TTGCGCGCTTAATCATTGC  72 UT_R ST258clade2_ SNP (G37 to T) ST258clade2_ GCTGACCTGCGGGTTGTTT  73 230 See Table 4 95%(12) 3 UT UT_F ST258clade2_ GCCACGATCTTCCTGCTGAA  74 UT_R ST340_UT SNP (C38 to A) ST340_UT_F TCGAGCCGGTTTGTTCATCG  75 256 See Table 4 97%(8) 3 ST340_UT_R CCGGACTACAGGACACTACA  76 ST380_UT SNP (C34 to T) ST380_UT_F GACAGTCACCCTTACCTACTA  77 300 See Table 4 97.5%(8) 3 CC ST380_UT_R CAGGTGGCCGGATTAAACTC  78 CG392_UT SNP (G37 to A) CG392_UT_F CATGCAGGGAGAAGGCAAA  79 255 See Table 4 96%(11) 3 CG392_UT_R ACCCAGGCGAAGCGATGTTC  80 See Table 3 ST395_UT SNP (C34 to T) ST395_UT_F CCCTTTGGGCGGCRCAT  81 261 Sequence type 97%(8) 3 not available ST395_UT_R AACGCTCAGGCGGAAGAC  82 ST437_UT SNP (G35 to T) ST437_UT_F CGACCATGATATGGCGGTGTT  83 290 See Table 4 97%(9) 3 C ST437_UT_R TGACCGCGCCTTTACGAT  84 AMR Gene Assays blaKPC_UT1 presence/ blaKPC_UT1_F CGTCTAGTTCTGCTGTCTTGT  85 338 TG79504 1 absence blaKPC_UT1_R ACCGTCATGCCTGTTGTC  86 blaKPC_UT2 presence/ blaKPC_UT2_F TTGTTGATTGGCTAAAGGGAA  87 133 TG79504 1 absence AC blaKPC_UT2_R CAGACGACGGCATAGTCATT  88 blaNDM_UT1 presence/ blaNDM_UT1_F GGACAAGATGGGCGGTATG  89 323 US-CA-2010b 1 absence (Bioproject PRHNA252957) blaNDM_UT1_R CGGCGTAGTGCTCAGTG  90 blaNDM_UT2 presence/ blaNDM_UT2_F CAACTGGATCAAGCAGGAGAT  91 130 US-CA-2010b 1 absence (Bioproject PRHNA252957) blaNDM_UT2_R CGACAACGCATTGGCATAAG  92 blaVIM_UT presence/ blaVIM_UT_F1 GGCGGCGTTGATGTCCTT  93 237 US-WA-2010 1 absence (Bioproject PRHNA252957) blaVIM_UT_R1 GGCACAACCACCGTATAGCA  94 blaVIM_UT_R2 CGCACAACCACCATAGAGCA  95 blaOXA-48_UT presence/ blaOXA-48_UT_ TGGCTCGAYGGTGGTATTCG  96 201 No positive 1 absence F1 available blaOXA-48_UT_ GGCTCGATGGCGGCATTC  97 F2 blaOXA-48_UT_ GACCCACCAGCCAATCTTAG  98 R1 blaOXA-48_UT_ GACCCACCAACCGATCTGAG  99 R2 blaCTX-M- presence/ blaCTX-M- CCGTCACGCTGTTGTTAGG 100 157 TG79504 1 G1_64_UT absence G1_64_UT_F blaCTX-M- CGCTCATCAGCACGATAAAGT 101 G1_64_UT_R blaCTX-M- presence/ blaCTX-M- GACGATGTCACTGGCTGAG 102 350 TG79504 1 G1_UT absence G1_UT2_F blaCTX-M- CCACAACCCAGGAAGCAG 103 G1_UT2_R blaCTX-M- presence/ blaCTX-M- TGGCGCAGACCCTGAAAA 104 181 US-NY-2005d 1 G2_UT1 absence G2_UT1_F (Bioproject PRJNA252957) blaCTX-M- ATATCGTTGGTGGTGCCATAA 105 G2_UT1_R blaCTX-M- presence/ blaCTX-M- ATGGCGCAGACCCTGAAA 106 158 US-NY-2005d 3 G2_UT2 absence G2_UT2_F (Bioproject PRJNA252957) blaCTX-M- CCGCTGCCGGTTTTATCG 107 G2_UT2_R blaCTX-M- presence/ blaCTX-M- GAGCCGACGCTCAACACC 108 201 No positive 1 G8_G25_UT1 absence G8G25_UT1_F available blaCTX-M- CCCGACAACCCACGATGT 109 G8G25_UT1_R blaCTX-M- presence/ blaCTX-M- GCTCAACACCGCGATCCC 110 193 No positive 3 G8_G25_UT2 absence G8G25_UT2_F available blaCTX-M- CCCGACAACCCACGATGT 111 G8G25_UT3_R blaCTX-M- presence/ blaCTX-M- TTCGTCTGGATCGCACTGA 112 374 TG28186 1 G9_UT1 absence G9_UT1_F (Escherichia coli) blaCTX-M- GATGATTCTCGCCGCTGAAG 113 G9_UT1_R blaCTX-M- presence/ blaCTX-M- CGCTGGTTCTGGTGACCTA 114  86 TG28186 1 G9_UT2 absence G9_UT2_F (Escherichia coli) blaCTX-M- GATGATTCTCGCCGCTGAAG 115 G9_UT2_R blaGES_UT presence/ blaGES_UT_F GGTGCAGCTTAGCGACAATG 116 275 No positive 1 absence available blaGES_UT_R CTCCCGTTTGGTTTCCGATCA 117 G gyrA_Kleb_ region of gyrA_Kleb_ CAATGACTGGAACAAAGCCT 118 170 susceptibe: 95%(9); also identifies 1 UT1 interest UT1_F TG22086 K. quasipneumoniae and (Bioproject K. variicola gyrA PRJEB7967) quinolone gyrA_Kleb_ CGATGGAACCAAAGTTACCC 119 resistant: resistance UT1_R TG22074 determining region at nucleotides 77-91. Wild type is SAVYD. parC_Kleb_ region of parC_Kleb_ CAGCGCGAAATTCAAAAAGT 120 180 susceptible: 97.5%(5) 1 UT2 interest UT2_F TG22074 quinolone parC_Kleb_ GCGAAAGATTTGGGATCGTC 121 resistant: resistance UT2_R No positive determining available region at nucleotides 77-85. Wild type is CYE. qnrA_UT presence/ qnrA_UT_F GATTTGAGYGACAGCCGTTT 122 297 Brazil-2009b 2 absence (Bioproject PRJNA252957) qnrA_UT_R GCAGAAGTACATCTTATGGCT 123 GA qnrC_UT presence/ qnrC_UT_F GCTAATTTCTCACAGGCAAAC 124  78 No positive 2 absence TTT available qnrC_UT_R ACAACCCGTAATGTAAGCAGA 125 G qnrD_UT presence/ qnrD_UT_F CGACAGGAATAGCTTGGAAGG 126 306 No positive 2 absence available qnrD_UT_R CCAGTTATCACAGTGCCATTC 127 qnrS_UT2 presence/ qnrS_UT_F GTGCTAACTTGCGTGATACGA 128 286 US-FL-2008 2 absence (Bioproject PRJNA252957) qnrS_UT_R1 TCCATATTGGCATAGGAAAGA 129 TTACA qnrS_UT_R2 TCCATATTGGCATAAGACAGG 130 TTACA qnrB-C1_UT presence/ qnrB-C1_UT_F CGACGTTCAGTGGTTCRGATC 131  61 TG22084 2 absence T qnrB-C1_UT_R GCKGCTCGCCAGTCGAAA 132 qnrB-C2_UT presence/ qnrB-C2_UT_F ACCAATCTAAGCTACGCCAAC 133  82 No positive Positive 2 absence TT available specimen analysis qnrB-C2_UT_R CCTGAGTTCCCATCCAGCG 134 qnrB-C3_UT presence/ qnrB-C3_UT_F CGCATATATCACCAATACCAA 135 281 TG41249 2 absence CTT (Providencia stuartii) qnrB-C3_UT_R GTTCCAGGAKCAACGATGCC 136 aac6-Ib_UT presence/ aac6-Ib_UT-F1 CCCAGTCGTACGTTGCTCTTG 137 303 aac6-Ib: 2 absence and TG22074 SNP (T36 to A or C AND G267 to T confers quinolone resistance rather than aminoglycoside resistance) aac6-Ib_UT_F2 GCTCAGTCGTACATTGCACTC 138 aac6-Ib-cr: US-VA-2007 (Bioproject PRJNA252957) aac6-Ib_UT_R CCTGGCGTGTTTGAACCATGT 139 AC aac3-II_UT presence/ aac3-II_UT_F CGCGTCGAACAGGTAGCA 140 210 TG79504 2 absence aac3-II_UT_R CGGTGGGTGACGTATGAGATG 141 aph3-I_UT presence/ aph3-I_UT_F GCGTTGCCAATGATGTTACAGA 142 277 TG22074 2 absence aph3-I_UT_R GCCTGAGCGAGACGAAATACG 143 aadB_UT presence/ aadB_UT_F GCGCGTCAYGGAGGAGTTG 144 268 US-MD-2006 2 absence (Bioproject PRJNA252957) aadB_UT_R TGCGAGCCTGTAGGACTCTA 145 aadA_UT presence/ aadA_UT_F GGCAGCGCAATGACATTCTTG 146 241 TG22074 2 absence aadA_UT_R CGGGACAACGTAAGCACTACA 147 arr_UT presence/ arr_UT_F1 CCACGGCGCTTTAAGTCCTC 148 245 TG22074 2 absence arr_UT-F2 CATGTAAACCACGACGTTTTA 149 AATCTTC arr_UT_R GGAGCTGAACTTGCTATGTCAC 150 T aadA5_UT presence/ aadA5_UT_F GCTGCGACACTGGACACAATC 151 211 Israel-2007b 2 absence (Bioproject PRJNA252957) aadA5_UT_R CGCTTCGAGCGACAACAGTTAG 152 armA presence/ armA_UT1_F ACTATTCTGCCTATCCTAATT 153 121 TG22074 2 absence GGG armA_UT1_R TCATTTAATGTTGCGACTCTTT 154 CA rmtA_UT1 presence/ rmtA_UT1_F GAATTGGACTGCCTCTACGATT 155 123 No positive 2 absence available rmtA_UT1_R GCACGCCCATACAGATGT 156 rmtB_UT1 presence/ rmtB_UT1_F AAGGCATGGAGGCGAAC 157 100 No positive 2 absence available rmtB_UT1_R AAGTATATAAGTTCTGTTCCG 158 ATGGT rmtC_UT1 presence/ rmtC_UT1_F AATACTCCACACTTTATCCAC 159  97 Guatemala- 2 absence CAA 2009 (Bioproject PRJNA252957) rmtC_UT1_R TTCTTGCGAACCTCCTTCTC 160 rmtD1&D2 presence/ rmtD1&D2_F AACGATGCGACGATCCATT 161 142 No positive 2 absence available rmtD1&D2_R GCGATTTGCTGTGCGAAA 162 npmA presence/ npmA_UT1_F CCGCTTGCTGGTACATATCTA 163 102 No positive Positive 2 absence available specimen analysis npmA_UT1_F CCTATCTCGTCCGCTATCTG 164 dfrA1_UT presence/ dfrA1_UT_F AATGGCTGTTGGTTGGACG 165  63 TG42433 2 absence drfA1_UT_R CATACTTTCGGTTGGGTAATG 166 CT dfrA15_UT presence/ dfrA15_UT_F AATATGCCGTTGTAACTCGTT 167 117 No positive 2 absence CA available dfrA15_UT_R ACACAATCACATGATCCGTTA 168 TCG dfrA16_UT presence/ dfrA16_UT_F AGTATGCAGTTGTAACTCGCT 169 129 No positive 2 absence CTA available dfrA16_UT_R CACCACCACCAGAAACGATAAC 170 dfrA14-30_UT presence/ dfrA14-30_UT_F GTGATTGGTTGCGGTCCA 171 261 US-PA-2001 2 absence (Bioproject PRJNA252957) dfrA14-30_UT_R CCCGCCACCAGACACTAT 172 DFRA6_31_UT presence/ dfrA6-31_UT_F YGAGAATGGAGTAATTGGCTCT 173 277 No positive 2 absence available dfrA6-31_UT_R WATTTCACCACCACCAGAAAC 174 AAA dfrA26-13_UT presence/ dfrA26-13_UT_F GGGWGCCAATCGGGTTAT 175  85 US-CA-2007a 2 absence (Bioproject PRJNA252957) dfrA26-13_UT_ CTCAGTGAGTCTGCGAAA 176 R1 dfrA26-13_UT_ CTCGGTGAGCCTGCGAAA 177 R2 dfrA8_UT presence/ dfrA8_UT_F AAAGACTACGAGCAGAATGGC 178  60 Brazil-2009b 2 absence (Bioproject PRJNA252957) dfrA8_UT_R ACGGTAAGTGAAGTAAGTGTG 179 AAG dfrA3b_UT presence/ dfrA3b_UT_F AACGCTGCCATTGTTACCA 180 107 No positive 2 absence available dfrA3b_UT_R AAGCCTTGAAGTGTTCTGGAG 181 dfrA9_UT presence/ dfrA9_UT_F AAGACAGGAGGTATCGGATTT 182 319 No positive 2 absence GA available dfrA9_UT_R CGTAGGCAGCTAAGTTCTCGTA 183 dfrA24_UT presence/ dfrA24_UT_F AAGACCGCATCAATATCGTCAT 184  60 No positive 2 absence C available dfrA24_UT_R CATAGCAAGCCGTCCAAGAA 185 dfrA27-28_UT presence/ dfrA27-28_UT_F AAGACTCTTACGAACCATGTTG 186 109 Colombia- 2 absence TT 2009a (Bioproject PRJNA252957) dfrA27-28_UT_R CCTCTGGCTCGGAATCTATTG 187 dfrA25_UT presence/ dfrA25_UT_F AAGCACTGACCTATAACCAATG 188 302 TG22010 2 absence G dfrA25_UT_R CCCAGGAATGTTCGGAAAGAAA 189 dfrA10_UT presence/ dfrA10_UT_F AAGCATTCAGAGACACAACCAA 190  51 TG21173 2 absence (Acineto- bacter baumannii) dfrA10_UT_R AACCAACACCACCAATGACAT 191 dfrA32_UT presence/ dfrA32_UT_F AAGGTGAGCAGCTAATCTTTA 192 134 No positive Positive 2 absence AGG available specimen analysis dfrA32_UT_R TGACCCTGAAATTCCATTCTT 193 TGA dfrA20_UT presence/ dfrA20_UT_F AAGTCGCACAACATCTTGAAG 194  63 No positive 2 absence G available dfrA20_UT_R AGATTTGAGCACCACCAATAA 195 TGA dfrA23_UT presence/ dfrA23_UT_F AATCAATATCACGACAGCGATC 196 222 No positive 2 absence AA available dfrA23_UT_R CTTCACGGGATGGGTCTCA 197 dfrA7_UT presence/ dfrA7_UT_F AATCAGTGGCTCCTTGTTGG 198  53 TG21968 2 absence dfrA7_UT_R GGAAGAACACCCATAGAGTCAA 199 AT dfrA29_UT presence/ dfrA29_UT_F AATCAGTGGCTTCTTGTCGG 200 246 No positive 2 absence available dfrA29_UT_R GTGGATGATAGATAAGTGGATG 201 GT dfrA17_UT presence/ dfrA17_UT_F AATGGCGTAATCGGTAGTGG 202 174 No positive Positive 2 absence available specimen analysis dfrA17_UT_R GCTTGAAATTCCGTTCTTTGAC 203 A dfrA18_UT presence/ dfrA18_UT_F ACGCATTGCTGTCATTGGT 204 160 US-MD-2005 2 absence (Bioproject PRJNA252957) dfrA18_UT_R CTCGCTGGCACTGGAATC 205 dfrA3_UT presence/ dfrA3_UT_R ACTCTATGCCGAGGCTCTG 206 186 No positive 2 absence available dfrA3_UT_R CGCTGACGACTCAAGGTAAC 207 dfrB1-8_UT presence/ dfrB1-8_UT_F WATGGGAGATCGCGTGCG 208  67 CAS813 2 absence (Bioproject PRJEB7967) dfrB1-8_UT_R GCWGTACCACCCGACAATCT 209 dfrB2-7_UT presence/ dfrB2-7_UT_F GCAGGGTCAAGTYGTCGG 210  66 No positive 3 absence available dfrB2-7_UT_R TCGGACTCGACSGCATAG 211 dfrB3_1_UT presence/ dfrB3_1_UT_F ACCCGACAACTTGACCCT 212 129 No positive 2 absence available dfrB3_1_UT_R ACCAACACAACAATGGAGTCA 213 dfrB4_UT presence/ dfrB4_UT_R AATCTCACCCAGGCTCAGT 214  50 No positive 2 absence available dfrB4_UT_R CCGTTCAAGCGCAGTCAT 215 sul1_UT presence/ sul1_UT_F GCTGGTGGTTATGCACTCAG 216 287 TG22074 2 absence sul1_UT_R CGCCCAAGAAGGATTTCCG 217 sul2_UT presence/ sul2_UT_F CATCATTTTCGGCATCGTCAAC 218 278 TG22074 2 absence sul2_UT_R GCGACAAGGCATAGGCTT 219 sul3_UT presence/ sul3_UT_F AAAGCCTTAATGACAGGTTTGA 220 110 US-IL-2009b 2 absence GT (Bioproject PRJNA252957) sul3_UT_R GAAGATGGAGCAGATGTGATTG 221 AT catA_UT presence/ catA_UT_F CGCAAGATGTGGCGTGTTAC 222 225 US-IL-2009b 2 absence (Bioproject PRJNA252957) catA_UT_R ARACGGCATGATGAACCTGAA 223 TC cmlA-B_UT presence/ cmlA-B_UT_F TCGCCACAGCGGTATCTG 224 216 TG22074 2 absence cmlA-B_UT_R GGGAAACACAAGACAGACCGA 225 floR_UT presence/ floR_UT_F1 GGCGACGGCCAATTCTACTTG 226 220 US-MO-2006 2 absence (Bioproject PRJNA252957) floR_UT_F2 GACGGCCGATCCTGCTTG 227 floR_UT_R1 AACGCCAGCAYCGAACTGAA 228 floR_UT_R2 AACGCCAGHATCGAACTGAA 229 mphA_UT presence/ mphA_UT_F GCCGATACCTCCCAACTGTAC 230 219 TG22074 2 absence mphA_UT_R GAACGGCAGGCGATTCTTG 231 strA_UT presence/ strA_UT_F GCGCTGCCCAGTTCTCTTC 232 279 TG22074 2 absence strA_UT_R CCCGCAATGCCGTCAATC 233 strB_UT presence/ strB_UT_F CGTTTCGCAACCTGTTCTCATT 234 217 TG22074 2 absence G strB_UT_R CCCGGCATATTCGAGCAACATC 235 mcr-1_UT presence/ mcr-1_UT_F TGGCAGCGACAAAGTCATC 236 273 No positive absence available mcr-1_UT_R TGCCGTGTATGTTCAGCTATC 237 tetA_UT presence/ tetA_UT_F1 TTGCCGCATTTGGCATTCTG 238 204 TG32076 2 absence tetA_UT_F2 CGCTTGCCGCATTTGGTATTC 239 tetA_UT_R GCGCCGGCATTCGA 240 tetB_UT presence/ tetB_UT_F TCGCTGCGTTGCTAAATATTGT 241 319 No positive 2 absence C available tetB_UT_R ATTCCAAGCCTTTGTGGCAGG 242 tetG_UT presence/ tetG_UT_F1 CCACGACCGTCGGCTTT 243 165 TG21548 2 absence tetG_UT_F2 CACCACGACTGTTGGTTTGTC 244 tetG_UT_F3 ACACCGCGACCGTTGGTTT 245 tetG_UT_R GCGTGRCAAAAGCCAGAAGA 246 tetD_UT presence/ tetD_UT_F TGAACAGCATTCTCGCTATCAA 247 251 TG20538 2 absence A (Escherichia tetD_UT_R CAGCCGCTTTCGTCAAACG 248 coli) Virulence Gene Assays rmpA_UT presence/ rmpA_UT_F AAGAGTATTGGTTGACWGCAGG 249 256 TG60548 3 absence ATT rmpA_UT_R TGTTAGCCGTGGATAATGGTTT 250 ACAA clbA- presence/ clbA- GCGAGCTTGGTGTCGATATTGA 251 322 TG60548 3 colibactin_ absence colibactin_ UT UT_F clbA- GTGATGAGTGGAGAGGCTAATG 252 colibactin C UT_R clbC- presence/ clbC- GCCGCCGAGTGATACAAGT 253 316 TG60548 3 colibactin_ absence colibactin_ UT UT_F clbC- GGTAGCAGGTTCATCCAGGTT 254 colibactin UT_R clbP- presence/ clbP- GCTATGCCTCCGCCAATTATGA 255 345 TG60548 3 colibactin_ absence colibactin_ UT UT_F clbP- CACTATTACCACGCCAACTGTT 256 colibactin ACT UT_R clbQ- presence/ clbQ- AGCCGCTGTGTCTTACGATG 257 258 TG60548 3 colibactin_ absence colibactin_ UT UT_F clbQ- CGATCTCTTCCATAAACGCCTG 258 colibactin AT UT_R iroB- presence/ iroB- AAACGACGGCGAACCCATT 259 182 TG60548 3 salmochelin_ absence salmochelin_ UT UT_F iroB- CGACTTCACTGGCGGAATCC 260 salmochelin_ UT_R irp2- presence/ irp2- ATTGCGGCGGACGAGAG 261 274 TG60548 3 yersinia- absence yersinia- bactin_UT bactin_UT_F irp2- GCTGACGACGGCGAACA 262 yersinia- bactin_UT_R ybtE- presence/ ybtE- CGCCGACATGCCGACTAT 263 319 TG60548 3 yersinia- absence yersinia- bactin_UT bactin_UT_F ybtE- CGCCGCCTGCCTGAAT 264 yersinia- bactin_UT_R ybtQ- presence/ ybtQ- GCAGAACCGATGGCGATGT 265 349 TG60548 3 yersinia- absence yersinia- bactin_UT bactin_UT_F ybtQ- GCGTCAGGCGGCGAATA 266 yersinia- bactin_UT_R ybtS- presence/ ybtS- GAAGAGTGTTATGTCTATGAGC 267 399 TG60548 3 yersinia- absence yersinia- GTCAA bactin_UT bactin_UT_F ybtS- TGCGTTCTGCGTCGTTGT 268 yersinia- bactin_UT_R iucD- presence/ iucD- GGCGGCAAGCGAGTCA 269 170 TG60548 3 aerobactin_ absence aerobactin_ UT UT_F iucD- TCAGGCGTGAAGTATTCGTTGG 270 aerobactin_ UT_R iutA- presence/ iutA- CCGAACTGGAACAGCAGATTCA 271 469 TG60548 3 aerobactin_ absence aerobactin_ UT UT_F iutA- GCATCGCCGTTACCGTCAA 272 aerobactin_ UT_R ABCt-00025_ presence/ ABCt-00025_ CCACTGGTAAACGGTTTATCCT 273 374 TG60548 3 UT absence UT_F1 C ABCt-00025_ CCGCTGGTAAAAGGTTTATCCT 274 UT_F2 C ABCt-00025_ GAACTGGCACMSAAATATCCC 275 UT_R CobW-00325_ presence/ CobW-00325_UT_ AACGACACTGCTTAACCACATC 276 254 TG60548 3 UT absence F1 CTGAA CobW-00325_UT_ AACGACACTGCTTAACCATATT 277 F2 CTGAA CobW-00325_UT_ CGGTGGACTCAATGACAAGCT 278 R1 CobW-00325_UT_ CGGTAGACTCAATAACAAGCT 279 R2 wzi_UT^(d) sequence- wzi_UT_F CGCGAGYGCTTTCTATCTTG 280 580 See Table 2 3 based wzi_UT_R GAGASCCACTGGTTCCAGAA 281 ^(a)Universal tail sequences are ACCCAACTGAATGGAGC (SEQ ID NO: 282) for forward read and ACGCACTTGACTTGTCTTC (SEQ ID NO: 283) for reverse read. The universal tail sequences precede the assay-specific primer sequence, for example, the primer sequence with the universal tail for the wzi_UT assay is ACCCAACTGAATGGAGCCGCGAGYGCTTTCTATCTTG (i.e., SEQ ID NO: 284 consisting of SEQ ID NOs: 280 and 282) for the forward primer and ACGCACTTGACTTGTCTTCGAGASCCACTGGTTCCAGAA (SEQ ID NO: 285 consting of SEQ ID NOs: 281 and 283) for the reverse primer. ^(b)CG35 is the only assay for which the identity threshold must be applied if the SNP state indicates CG35 is present (Some strains of Enterobacter aerogenes amplify and have C34T for this target). For all other assays, the canonical SNP state is specific to that clonal group of K. pneumoniae; the identity threshold just makes the assay Klebsiella-specific. ^(c)CG258wo395 is the assay that captures all of CG258 except for ST395 (as shown in FIG. 4). ^(d)From Bowers J R, Kitchel B, Driebe E M, MacCannell D R, Roe C, Lemmer D, de Man T, Rasheed J K, Engelthaler D M, Klein P, Limbago B M. 2015. Genomic Analysis of the Emergence and Rapid Global Dissemination of the Clonal Group 258 Klebsiella pneumoniae Pandemic. PLoS One 10: e0133727. ^(e)From Brisse S, Passet V, Haugaard A B, Babosan A, Kassis-Chikhani N, Struve C, Decre D. 2013. wzi Gene sequencing, a rapid method for determination of capsular type for Klebsiella strains, J Clin Microbiol 51: 4073-4078.

TABLE 5 In-house genomes used for KlebSeq strain identification validaton. K. pneumoniae Sample Species sequence type Accession information 8045 K. pneumoniae 82 Bioproject PRJEB7967 A5054 K. pneumoniae 82 Bioproject PRJEB7967 Brazil-2009b K. pneumoniae ST437 Bioproject PRJNA252957 C3091 K. pneumoniae NF Bioproject PRJEB7967 Canada-2009a K. pneumoniae 512 Bioproject PRJNA252957 Canada-2009b K. pneumoniae 20 Bioproject PRJNA252957 Canada-2009c K. pneumoniae 152 Bioproject PRJNA252957 Canada-2009d K. pneumoniae SLVST815 Bioproject PRJNA252957 CAS698 K. pneumoniae 23 Bioproject PRJEB7967 CAS726 K. pneumoniae 23 Bioproject PRJEB7967 CAS727 K. pneumoniae 23 Bioproject PRJEB7967 CAS813 K. pneumoniae 23 Bioproject PRJEB7967 Guatemala-2009 K. pneumoniae 11 Bioproject PRJNA252957 India-2007a K. pneumoniae 101 Bioproject PRJNA252957 India-2007b K. pneumoniae 43 Bioproject PRJNA252957 Israe1-2007a K. pneumoniae 512 Bioproject PRJNA252957 Israe1-2007b K. pneumoniae 277 Bioproject PRJNA252957 Israe1-2007c K. pneumoniae 340 Bioproject PRJNA252957 Israe1-2007d K. pneumoniae 376 Bioproject PRJNA252957 Sp221 K. pneumoniae 249 Bioproject PRJEB7967 Sp29 K. pneumoniae 249 Bioproject PRJEB7967 TG22074 K. pneumoniae 15 TBD* TG22084 K. pneumoniae 15 TBD* TG22086 K. pneumoniae 34 Bioproject PRJEB7967 TG22092 K. variicola 2006 TBD* TG28459 K. pneumoniae 36 Bioproject PRJEB7967 TG31708 K. pneumoniae 23 TBD* TG31716 K. pneumoniae 23 TBD* TG31732 K. pneumoniae 23 TBD* TG31736 K. pneumoniae 260 TBD* TG32076 K. pneumoniae 42 TBD* TG64566 K. pneumoniae 101 TBD* TG64698 K. pneumoniae 23 TBD* TG65600 K. pneumoniae 2055 TBD* TG69833 K. pneumoniae 36 TBD* TG69835 K. pneumoniae 111 TBD* TG69845 K. pneumoniae 776 TBD* TG77275 K. pneumoniae 636 TBD* TG77291 K. quasipneumoniae 978 TBD* TG79500 K. pneumoniae 1401 TBD* TG79504 K. pneumoniae Unknown TBD* TG79508 K. pneumoniae 380 TBD* TG79512 K. pneumoniae SLV of ST34 TBD* TG79516 K. pneumoniae Unknown TBD* TG79520 K. pneumoniae 107 TBD* US-CA-2007a K. pneumoniae 340 Bioproject PRJNA252957 US-CA-2008 K. pneumoniae 833 Bioproject PRJNA252957 US-CA-2010a K. pneumoniae 11 Bioproject PRJNA252957 US-CA-2010b K. pneumoniae 37 Bioproject PRJNA252957 US-CA-2011 K. pneumoniae 14 Bioproject PRJNA252957 US-FL-2008 K. pneumoniae SLVST513 Bioproject PRJNA252957 US-GA-2006b K. pneumoniae 20 Bioproject PRJNA252957 US-GA-2009b K. variicola 1 SNP from ST360 Bioproject PRJNA252957 US-IL-2008b K. pneumoniae 14 Bioproject PRJNA252957 US-IL-2009a K. pneumoniae 258 Bioproject PRJNA252957 US-IL-2009b K. pneumoniae 258 Bioproject PRJNA252957 US-MD-2005 K. pneumoniae 228 Bioproject PRJNA252957 US-MD-2006 K. pneumoniae 11 Bioproject PRJNA252957 US-MD-2011 K. pneumoniae 14 Bioproject PRJNA252957 US-MI-2008 K. pneumoniae 14 Bioproject PRJNA252957 US-MO-2006 K. pneumoniae 14 Bioproject PRJNA252957 US-NC-1996 K. pneumoniae 37 Bioproject PRJNA252957 US-NM-2007 K. pneumoniae 258 Bioproject PRJNA252957 US-NY-2004a K. pneumoniae 234 Bioproject PRJNA252957 US-NY-2004c K. pneumoniae SLVST244 Bioproject PRJNA252957 US-NY-2004d K. pneumoniae 42 Bioproject PRJNA252957 US-NY-2005b K. pneumoniae 65 Bioproject PRJNA252957 US-NY-2005c K. pneumoniae ST258 clade 1 Bioproject PRJNA252957 US-NY-2009a K. pneumoniae ST258 clade 1 Bioproject PRJNA252957 US-PA-2001 K. quasipneumoniae 334 Bioproject PRJNA252957 US-SD-2012 K. pneumoniae 258 Bioproject PRJNA252957 US-TX-2001 K. pneumoniae SLVST427 Bioproject PRJNA252957 US-TX-2011 K. pneumoniae 39 Bioproject PRJNA252957 US-VA-2007 K. pneumoniae 45 Bioproject PRJNA252957 US-VA-2008a K. pneumoniae ST258 clade 1 Bioproject PRJNA252957 US-VA-2008b K. pneumoniae 719 Bioproject PRJNA252957 US-WA-2010 K. pneumoniae 147 Bioproject PRJNA252957 TG75900 K. quasipneumoniae 196 TBD* 8045 K. pneumoniae 82 Bioproject PRJEB7967 A5054 K. pneumoniae 82 Bioproject PRJEB7967 Brazil-2009b K. pneumoniae ST437 Bioproject PRJNA252957 C3091 K. pneumoniae NF Bioproject PRJEB7967 Canada-2009a K. pneumoniae 512 Bioproject PRJNA252957 Canada-2009b K. pneumoniae 20 Bioproject PRJNA252957 Canada-2009c K. pneumoniae 152 Bioproject PRJNA252957 Canada-2009d K. pneumoniae SLVST815 Bioproject PRJNA252957 CAS698 K. pneumoniae 23 Bioproject PRJEB7967 CAS726 K. pneumoniae 23 Bioproject PRJEB7967 CAS727 K. pneumoniae 23 Bioproject PRJEB7967 CAS813 K. pneumoniae 23 Bioproject PRJEB7967 Guatemala-2009 K. pneumoniae 11 Bioproject PRJNA252957 India-2007a K. pneumoniae 101 Bioproject PRJNA252957 India-2007b K. pneumoniae 43 Bioproject PRJNA252957 Israel-2007a K. pneumoniae 512 Bioproject PRJNA252957 Israel-2007b K. pneumoniae 277 Bioproject PRJNA252957 Israel-2007c K. pneumoniae 340 Bioproject PRJNA252957 Israel-2007d K. pneumoniae 376 Bioproject PRJNA252957 Sp221 K. pneumoniae 249 Bioproject PRJEB7967 Sp29 K. pneumoniae 249 Bioproject PRJEB7967 TG22074 K. pneumoniae 15 TBD* TG22084 K. pneumoniae 15 TBD* TG22086 K. pneumoniae 34 Bioproject PRJEB7967 TG22092 K. variicola 2006 TBD* TG28459 K. pneumoniae 36 Bioproject PRJEB7967 TG31708 K. pneumoniae 23 TBD* TG31716 K. pneumoniae 23 TBD* TG31732 K. pneumoniae 23 TBD* TG31736 K. pneumoniae 260 TBD* TG32076 K. pneumoniae 42 TBD* TG64566 K. pneumoniae 101 TBD* TG64698 K. pneumoniae 23 TBD* TG65600 K. pneumoniae 2055 TBD* TG69833 K. pneumoniae 36 TBD* TG69835 K. pneumoniae 111 TBD* TG69845 K. pneumoniae 776 TBD* TG77275 K. pneumoniae 636 TBD* TG77291 K. quasipneumoniae 978 TBD* TG79500 K. pneumoniae 1401 TBD* TG79504 K. pneumoniae Unknown TBD* TG79508 K. pneumoniae 380 TBD* TG79512 K. pneumoniae SLV of ST34 TBD* TG79516 K. pneumoniae Unknown TBD* TG79520 K. pneumoniae 107 TBD* US-CA-2007a K. pneumoniae 340 Bioproject PRJNA252957 US-CA-2008 K. pneumoniae 833 Bioproject PRJNA252957 US-CA-2010a K. pneumoniae 11 Bioproject PRJNA252957 US-CA-2010b K. pneumoniae 37 Bioproject PRJNA252957 US-CA-2011 K. pneumoniae 14 Bioproject PRJNA252957 US-FL-2008 K. pneumoniae SLVST513 Bioproject PRJNA252957 US-GA-2006b K. pneumoniae 20 Bioproject PRJNA252957 US-GA-2009b K. variicola 1 SNP from ST360 Bioproject PRJNA252957 US-IL-2008b K. pneumoniae 14 Bioproject PRJNA252957 US-IL-2009a K. pneumoniae 258 Bioproject PRJNA252957 US-IL-2009b K. pneumoniae 258 Bioproject PRJNA252957 US-MD-2005 K. pneumoniae 228 Bioproject PRJNA252957 US-MD-2006 K. pneumoniae 11 Bioproject PRJNA252957 US-MD-2011 K. pneumoniae 14 Bioproject PRJNA252957 US-MI-2008 K. pneumoniae 14 Bioproject PRJNA252957 US-MO-2006 K. pneumoniae 14 Bioproject PRJNA252957 US-NC-1996 K. pneumoniae 37 Bioproject PRJNA252957 US-NM-2007 K. pneumoniae 258 Bioproject PRJNA252957 US-NY-2004a K. pneumoniae 234 Bioproject PRJNA252957 US-NY-2004c K. pneumoniae SLVST244 Bioproject PRJNA252957 US-NY-2004d K. pneumoniae 42 Bioproject PRJNA252957 US-NY-2005b K. pneumoniae 65 Bioproject PRJNA252957 US-NY-2005c K. pneumoniae ST258 clade 1 Bioproject PRJNA252957 US-NY-2009a K. pneumoniae ST258 clade 1 Bioproject PRJNA252957 US-PA-2001 K. quasipneumoniae 334 Bioproject PRJNA252957 US-SD-2012 K. pneumoniae 258 Bioproject PRJNA252957 US-TX-2001 K. pneumoniae SLVST427 Bioproject PRJNA252957 US-TX-2011 K. pneumoniae 39 Bioproject PRJNA252957 US-VA-2007 K. pneumoniae 45 Bioproject PRJNA252957 US-VA-2008a K. pneumoniae ST258 clade 1 Bioproject PRJNA252957 US-VA-2008b K. pneumoniae 719 Bioproject PRJNA252957 US-WA-2010 K. pneumoniae 147 Bioproject PRJNA252957 TG75900 K. quasipneumoniae 196 TBD* *Uploaded this study

In one aspect, the clonal group and/or subgroup detected is one or more of those shown in Table 6.

TABLE 6 Clonal subgroup Assay name SEQ ID NOs CG258 CG258 CG258_UT 63/64 CG258wo395_UT 65/66 ST258 ST258_UT1 67/68 ST258_UT2 69/70 ST258clade1_UT 71/72 ST258clade2_UT 73/74 ST340 ST340_UT 75/76 ST395 ST395_UT 81/82 ST437 ST437_UT 83/84 CG20 CG20_UT 21/22 ST20 ST20_UT 23/24 ST23 ST23_UT 25/26 ST380 ST380_UT 77/78 CG37 CG37_UT 37/38 CG14 CG14_UT 13/14 ST14 ST14_UT 15/16 innerST14_UT 17/18 ST15 ST15_UT 19/20

In another aspect, the AMR gene detected is one or more of those shown in Table 7.

TABLE 7 AMR genes Assay name SEQ ID NOs beta-lactamase genes c blaKPC_UT1 85/86 blaKPC_UT2 87/88 blaNDM_UT1 89/90 blaNDM_UT2 91/92 blaVIM_UT  93/94-95 blaOXA-48_UT 96-97/98-99 blaCTX-M-G1_64_UT 100/101 blaCTX-M-G1_UT 102/103 blaCTX-M-G2_UT1 104/105 blaCTX-M-G2_UT2 106/107 blaCTX-M-G8_G25_UT1 108/109 blaCTX-M-G8_G25_UT2 110/111 blaCTX-M-G9_UT1 112/113 blaCTX-M-G9_UT2 114/115 blaGES_UT 116/117 colistin resistance gene mcr-1_UT 236/237

In yet another aspect, the virulence gene detected is one or more of those shown in Table 8.

TABLE 8 Virulence SEQ genes Assay name ID NOs rmpA blaKPC_UT1 249/250 wzi wzi_UT 280/281

Unless defined otherwise, all technical and scientific terms herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although any methods and materials, similar or equivalent to those described herein, can be used in the practice or testing of the present invention, the preferred methods and materials are described herein. All publications, patents, and patent publications cited are incorporated by reference herein in their entirety for all purposes.

The publications discussed herein are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that the present invention is not entitled to antedate such publication by virtue of prior invention.

While the invention has been described in connection with specific embodiments thereof, it will be understood that it is capable of further modifications and this application is intended to cover any variations, uses, or adaptations of the invention following, in general, the principles of the invention and including such departures from the present disclosure as come within known or customary practice within the art to which the invention pertains and as may be applied to the essential features hereinbefore set forth and as follows in the scope of the appended claims.

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Division of     Microbiology Devices, U.S. Food and Drug Administration, Rockville,     Md. 

What is claimed is:
 1. A method of detecting one or more Klebsiella species within a sample from a subject, the method comprising: selecting a primer pair, wherein each primer of the primer pair comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 5-10; subjecting DNA, RNA, or both from the sample to a PCR amplification reaction using the primer pair; and detecting the Klebsiella species by detecting amplification products resulting from the PCR amplification reaction.
 2. The method of claim 1, wherein the one or more Klebsiella species are selected from the group consisting of: K. quasipneumoniae, K. oxytoca, and K. variicola.
 3. The method of claim 1, further comprising: selecting a second primer pair from the group consisting of: primers with a nucleic acid sequence comprising a sequence set forth in SEQ ID NOs: 11-84; subjecting the DNA, RNA, or both from the sample to a PCR amplification reaction using the second primer pair, and detecting the Klebsiella clonal group by detecting amplification products resulting from the PCR amplification reaction, wherein the amplification products resulting from the PCR amplification comprises a Klebsiella clonal group-specific canSNP.
 4. The method of claim 3, wherein the amplification products resulting from the PCR amplification using the primer pair comprises the clonal group-specific canSNP selected from the group consisting of: CG258 and its subgroups, CG20 and its subgroup ST20, ST23, ST380, CG37, and CG14 and its subgroups.
 5. The method of claim 4, wherein each primer of the primer pair comprises a nucleic acid sequence selected from the group consisting of: SEQ ID NOs: 13-26, 37-38, 63-78, and 81-84.
 6. The method of claim 1, further comprising: selecting a primer pair targeting an antimicrobial resistance (AMR) gene in the Klebsiella species, wherein each primer of the primer pair targeting an AMR gene comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 85-248; subjecting the DNA, RNA, or both from the sample to a PCR amplification reaction using a primer pair targeting the AMR gene, and detecting the AMR gene.
 7. The method of claim 6, wherein the primer pair targets a beta-lactamase gene, a colistin resistance gene, or both.
 8. The method of claim 7, wherein the colistin resistance gene is mcr-1.
 9. The method of claim 7, wherein each primer of the primer pair targeting the beta-lactamase gene comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 85-117, and the primer pair targeting the colistin resistance gene contains sequences selected from the group consisting of SEQ ID NOs: 236-237.
 10. The method of claim 1, further comprising: selecting a primer pair targeting a virulence gene in the Klebsiella species, wherein each primer of the primer pair targeting the virulence gene in the Klebsiella species comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 249-281; subjecting the DNA, RNA, or both from the sample to a PCR amplification reaction using the primer pair targeting the virulence gene, and detecting the virulence gene.
 11. The method of claim 10, wherein the primer pair targets rmpA, wzi, or both, each primer of the primer pair targeting rmpA comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 249-250, and each pair of the primer pair targeting wzi comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 280-281.
 12. The method of claim 1, wherein the PCR amplification reaction is a multiplex amplification reaction.
 13. The method of claim 1, wherein the amplification products of PCR amplification reaction are detected by next-generation sequencing (NGS).
 14. The method of claim 1, wherein the subject has pneumonia, the method further comprises treating the subject with an aminoglycoside, cephalosporin, or both upon detection of the Klebsiella species.
 15. A composition for detecting one or more Klebsiella species comprising: a primer pair, wherein the nucleic acid sequence of each primer of the primer pair comprises a sequence selected from the group consisting of: SEQ ID NOs: 5-10; and a universal tail sequence comprising a sequence selected from the group consisting of SEQ ID NOs: 282-283; and a nucleotide polymerase, buffer, diluent, excipient, or combinations thereof.
 16. The composition of claim 15, further comprising a primer pair for detecting a Klebsiella clonal group, wherein the nucleic acid sequence of each primer of the primer pair for detecting the Klebsiella clonal group is selected from the group consisting of: SEQ ID NOs: 11-84.
 17. The composition of claim 15, further comprising a primer pair for detecting an AMR gene in the Klebsiella species, wherein the nucleic acid sequence of each primer of the primer pair for detecting the AMR gene in the Klebsiella species is selected from the group consisting of: SEQ ID NOs: 85-248.
 18. The composition of claim 15, further comprising a primer pair for detecting a virulence gene in the Klebsiella species, wherein the nucleic acid sequence of each primer of the primer pair for detecting the virulence gene in the Klebsiella species is selected from the group consisting of: SEQ ID NOs: 249-281.
 19. A composition for detecting one or more Klebsiella species comprising a primer pair, wherein the nucleic acid sequence of each primer of the primer pair comprises a sequence selected from the group consisting of: SEQ ID NOs: 5-10; and a universal tail sequence comprising a sequence selected from the group consisting of SEQ ID NOs: 282-283. 